Proteopedia - User contributions [en]

CBI Molecules

2014-12-03T19:34:49Z

Vanessa Chaplin:

These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].
Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

Fall 2014: CBI Molecules are due 12/3/14 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2014" or "Revised 2014". For those editing an existing CBI Molecule, start by making a copy of that entry (leaving the original intact) so that it retains the full author list of all authors that contributed (or include credits and a link to the original page and authors if it does not).
Follow the instructions at the bottom of this page.

==Molecules==
'''** Designates CBI Molecules Featured on [http://www.umass.edu/cbi/ CBI website]'''

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

[http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]

: '''[[Molecular Playground/ClyA]]''', Bib Yang
: '''[[Molecular Playground/OmpG]]''', Christina Chisholm

[http://openwetware.org/wiki/Chien Chien Lab]

: '''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi
: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau '''Best CBI Molecule 2011'''
: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu

Farkas Lab
: '''[[Molecular Playground/CLOCK:BMAL1 heterodimer complex]]''', Hui-Hsien Lin, Joseph Hardie, Michael Mingroni '''New 2014'''

Forbes Lab

: '''[[Molecular Playground/CheR]]''', Miaomin Zhang
: '''[[Molecular Playground/RBP]]''', Jan Panteli
: '''[[Molecular Playground/TRAIL]]''', Charley Swofford

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon
: '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli

[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]

: '''[[Molecular_Playground/DnaK]]''', Joseph Tilitsky, New 2014
: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy '''Best Overall CBI Molecule 2010'''
: '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez
: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani '''Best CBI Molecule 2012'''

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill
: '''[[Molecular Playground/Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao
: '''[[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay
: '''[[Molecular Playground/Caspase-7 Dynamics]]'''
: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber
: '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez
: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls
: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

: '''[[Molecular_Playground/Hsp70-Hsp90]]''', Jill Graham
: '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben
: '''[[Molecular Playground/Saposin C]]''', Abla Tannous
: '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]

: '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez, Yuzhou Tang

[http://people.chem.umass.edu/mholden/ Holden Lab]

: '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]

: '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]'''[Revised], Chengfeng Ren
: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski
: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita
: '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao

[http://people.chem.umass.edu/knapplab/?q=knappchem/index.html/ Knapp Lab]
: '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas '''Best CBI Molecule Proteopedia Page 2010''' '''***New Fall 2014***'''
: '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky

[http://people.chem.umass.edu/mmaroney/ Maroney Lab]

: '''[[Molecular Playground/UreE]]''', Priyanka Basak, '''New 2014'''
: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, '''Revised 2014'''
: '''[[Molecular Playground/HypA]]''', Heidi Hu

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia '''Best CBI Molecule 2011'''
: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia
: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

[http://www.peytonlab.org/ Peyton Lab]
: '''[[Molecular Playground/IntegrinBeta1]]''', Lauren Jansen, Lauren Barney, Elizabeth Brooks, Alyssa Schwartz ***'''NEW FALL 2014''''***
: '''[[Molecular Playground/MMP14]]''', Lauren Jansen
: '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman

[http://roberts.openwetware.org/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson
: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino
: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang
: '''[[Molecular playground/Chymotrypsin]]''', Brad
: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

[http://http://www.umass.edu/schiffman/ Schiffman Lab]
: '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

[http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]
: '''[[Molecular Playground/Tic40]]''', Mine Canakci

Tew Lab

: '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde

Thayumanavan Lab
: '''[[Interleukin-1 beta]]''', Huan He
: '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez
: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura
: '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi
: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy
: '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado
: '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang
: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo
: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

[http://people.chem.umass.edu/thompson/index.html Thompson Lab]

: '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi
: '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin
: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones
: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

[http://www.chem.umass.edu/~vachet/index.html Vachet Lab]

: ''[[Molecular Playground/Human Serum Albumin]]''', Mahalia Serrano
: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto '''Best CBI Molecule Jmol scenes 2010'''
: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou
:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne
: '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

:'''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab
: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab
: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad, Schnarr lab

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang, Weis lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab
: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab

: '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

==Instructions==

'''The goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''

Fall 2014: Complete steps 1-3 before the CBI Molecule Workshop on 11/19; bring your computer to the CBI Molecule Workshop in ISB 321. You will be able to start work on your CBI Molecule at the workshop. You should plan to stay and finish your molecule after the workshop (or as soon as possible) while the instructions and ideas are fresh in your mind.

A successful CBI Molecule is an interesting, nontechnical description of a molecule related to your group's research. It should tell an interesting story with few words and many green scenes. Green scenes should be clear and attractive illustrations that tell your story. It's great if you can end with a brief statement about how it relates to your group's research goals.

1. If you don't already have one, request a Proteopedia account and log in.

2. Read through the rest of the instructions, do the tutorials below, and look at any existing CBI Molecules from your research group. Talk with other CBI students in your research group and decide how you will collaborate to make an improved CBI Molecule related to your group's research. Develop ideas for the scenes that each of you will make.

3. Get started working in Proteopedia. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. Explore the HELP links below to learn how to make a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made).

'''Complete the above steps before the CBI Molecule Workshop.'''

4. When editing an existing CBI Molecule, leave the original intact and make a copy that you will edit so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the CBI Molecules, but everyone will need to log in as themself and create a green scene to get credit for their work and to appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.

5. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished, and then "new 2014" or "revised 2014". Minimize text; tell your story with green scenes!

6. When your CBI Molecule is complete, send Lynmarie an email to nominate a cool scene/clever caption you would like to feature at the Molecular Playground (include a link to your CBI Molecule, name of the green scene, and caption).

==Links to HELP pages==
Overview at [[Help:Contents ]]

See also [[Help:Getting_Started_in_Proteopedia]]

Videos showing how to use Proteopedia:
[[Proteopedia:Video_Guide]]
(Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)

[[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]
gives succinct step by step instructions on how to create a molecular scene.

A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.
[http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]

[[Proteopedia:Guidelines for Ethical Writing]].
Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.

For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.

CBI Molecules

2014-12-03T19:32:27Z

Vanessa Chaplin:

These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].
Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

Fall 2014: CBI Molecules are due 12/3/14 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2014" or "Revised 2014". For those editing an existing CBI Molecule, start by making a copy of that entry (leaving the original intact) so that it retains the full author list of all authors that contributed (or include credits and a link to the original page and authors if it does not).
Follow the instructions at the bottom of this page.

==Molecules==
'''** Designates CBI Molecules Featured on [http://www.umass.edu/cbi/ CBI website]'''

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

[http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]

: '''[[Molecular Playground/ClyA]]''', Bib Yang
: '''[[Molecular Playground/OmpG]]''', Christina Chisholm

[http://openwetware.org/wiki/Chien Chien Lab]

: '''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi
: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau '''Best CBI Molecule 2011'''
: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu

Farkas Lab
: '''[[Molecular Playground/CLOCK:BMAL1 heterodimer complex]]''', Hui-Hsien Lin, Joseph Hardie, Michael Mingroni '''New 2014'''

Forbes Lab

: '''[[Molecular Playground/CheR]]''', Miaomin Zhang
: '''[[Molecular Playground/RBP]]''', Jan Panteli
: '''[[Molecular Playground/TRAIL]]''', Charley Swofford

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon
: '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli

[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]

: '''[[Molecular_Playground/DnaK]]''', Joseph Tilitsky, New 2014
: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy '''Best Overall CBI Molecule 2010'''
: '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez
: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani '''Best CBI Molecule 2012'''

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill
: '''[[Molecular Playground/Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao
: '''[[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay
: '''[[Molecular Playground/Caspase-7 Dynamics]]'''
: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber
: '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez
: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls
: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

: '''[[Molecular_Playground/Hsp70-Hsp90]]''', Jill Graham
: '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben
: '''[[Molecular Playground/Saposin C]]''', Abla Tannous
: '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]

: '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez, Yuzhou Tang

[http://people.chem.umass.edu/mholden/ Holden Lab]

: '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]

: '''[http://proteopedia.org/wiki/index.php/Chengfeng_Ren Molecular Playground/Inteferon]'''[Revised], Chengfeng Ren
: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski
: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita
: '''[[Molecular Playground/Antithrombin-Heparin]]''', Yunlong Zhao

Knapp lab
: '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas '''Best CBI Molecule Proteopedia Page 2010''' ***New Fall 2014***
: '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky

[http://people.chem.umass.edu/mmaroney/ Maroney Lab]

: '''[[Molecular Playground/UreE]]''', Priyanka Basak, '''New 2014'''
: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr, Hsin-Ting (Tiffany )Huang, '''Revised 2014'''
: '''[[Molecular Playground/HypA]]''', Heidi Hu

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia '''Best CBI Molecule 2011'''
: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia
: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

[http://www.peytonlab.org/ Peyton Lab]
: '''[[Molecular Playground/IntegrinBeta1]]''', Lauren Jansen, Lauren Barney, Elizabeth Brooks, Alyssa Schwartz ***'''NEW FALL 2014''''***
: '''[[Molecular Playground/MMP14]]''', Lauren Jansen
: '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman

[http://roberts.openwetware.org/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson
: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino
: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang
: '''[[Molecular playground/Chymotrypsin]]''', Brad
: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

[http://http://www.umass.edu/schiffman/ Schiffman Lab]
: '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

[http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]
: '''[[Molecular Playground/Tic40]]''', Mine Canakci

Tew Lab

: '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde

Thayumanavan Lab
: '''[[Interleukin-1 beta]]''', Huan He
: '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez
: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura
: '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi
: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy
: '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado
: '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang
: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo
: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

[http://people.chem.umass.edu/thompson/index.html Thompson Lab]

: '''[[Molecular Playground/Bacterial Chemotaxis Complex]]''', Elizabeth R. Haglin, Maryam Kashefi
: '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin
: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones
: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

[http://www.chem.umass.edu/~vachet/index.html Vachet Lab]

: ''[[Molecular Playground/Human Serum Albumin]]''', Mahalia Serrano
: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto '''Best CBI Molecule Jmol scenes 2010'''
: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou
:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne
: '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

:'''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey, Schnarr lab
: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey, Schnarr lab
: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad, Schnarr lab

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang, Weis lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffi, Bhatia Lab
: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer, Bhatia Lab

: '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

==Instructions==

'''The goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''

Fall 2014: Complete steps 1-3 before the CBI Molecule Workshop on 11/19; bring your computer to the CBI Molecule Workshop in ISB 321. You will be able to start work on your CBI Molecule at the workshop. You should plan to stay and finish your molecule after the workshop (or as soon as possible) while the instructions and ideas are fresh in your mind.

A successful CBI Molecule is an interesting, nontechnical description of a molecule related to your group's research. It should tell an interesting story with few words and many green scenes. Green scenes should be clear and attractive illustrations that tell your story. It's great if you can end with a brief statement about how it relates to your group's research goals.

1. If you don't already have one, request a Proteopedia account and log in.

2. Read through the rest of the instructions, do the tutorials below, and look at any existing CBI Molecules from your research group. Talk with other CBI students in your research group and decide how you will collaborate to make an improved CBI Molecule related to your group's research. Develop ideas for the scenes that each of you will make.

3. Get started working in Proteopedia. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. Explore the HELP links below to learn how to make a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made).

'''Complete the above steps before the CBI Molecule Workshop.'''

4. When editing an existing CBI Molecule, leave the original intact and make a copy that you will edit so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the CBI Molecules, but everyone will need to log in as themself and create a green scene to get credit for their work and to appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.

5. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished, and then "new 2014" or "revised 2014". Minimize text; tell your story with green scenes!

6. When your CBI Molecule is complete, send Lynmarie an email to nominate a cool scene/clever caption you would like to feature at the Molecular Playground (include a link to your CBI Molecule, name of the green scene, and caption).

==Links to HELP pages==
Overview at [[Help:Contents ]]

See also [[Help:Getting_Started_in_Proteopedia]]

Videos showing how to use Proteopedia:
[[Proteopedia:Video_Guide]]
(Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)

[[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]
gives succinct step by step instructions on how to create a molecular scene.

A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.
[http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]

[[Proteopedia:Guidelines for Ethical Writing]].
Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.

For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.

Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme

2014-12-03T19:30:13Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

These HIF-hydroxylase enzymes include the Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both. <ref>PMID:12615973</ref> This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" /> PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates either the Pro-402 or Pro-564 residue in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A HIF-α] whereas PHD3 can only hydroxylate the Pro-564 position.

Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ PHD2]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (as mentioned above) in [http://en.wikipedia.org/wiki/HIF1A HIF-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref> Our goal in the Knapp Lab is to understand and define the mechanism of action for this enzyme and evaluate how oxygen affects enzyme activity to improve knowledge of oxygen sensing.

<structure load='2g19' size='335' frame='true' align='right'
caption='Significant structural features of Prolyl Hydroxylase Domain-2 (PHD-2) enzyme. PDB Codes: [[2g19]] and 3HQR.' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain 2 (PHD2) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions such as Fenton chemistry.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 (shown in purple) undergoes a large <scene name='60/609795/B2b3_loop_with_cood/1'>conformational change</scene>. The β2β3 loop moves toward the active site and closes over the active site entrance. This loop movement is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. Hydroxylation occurs within the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A HIF-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of HIF-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results in degradation of HIF-α by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A HIF-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme

2014-12-03T19:28:22Z

Vanessa Chaplin:

'''Bold text'''One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

These HIF-hydroxylase enzymes include the Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both. <ref>PMID:12615973</ref> This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" /> PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates either the Pro-402 or Pro-564 residue in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A HIF-α] whereas PHD3 can only hydroxylate the Pro-564 position.

Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ PHD2]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (as mentioned above) in [http://en.wikipedia.org/wiki/HIF1A HIF-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref> Our goal in the Knapp Lab is to understand and define the mechanism of action for this enzyme and evaluate how oxygen affects enzyme activity to improve knowledge of oxygen sensing.

<structure load='2g19' size='335' frame='true' align='right'
caption='Significant structural features of Prolyl Hydroxylase Domain-2 (PHD-2) enzyme [[2g19]] and 3HQR' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain 2 (PHD2) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions such as Fenton chemistry.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 (shown in purple) undergoes a large <scene name='60/609795/B2b3_loop_with_cood/1'>conformational change</scene>. The β2β3 loop moves toward the active site and closes over the active site entrance. This loop movement is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. Hydroxylation occurs within the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A HIF-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of HIF-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results in degradation of HIF-α by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A HIF-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-12-03T19:27:06Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

These HIF-hydroxylase enzymes include the Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both. <ref>PMID:12615973</ref> This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" /> PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates either the Pro-402 or Pro-564 residue in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A HIF-α] whereas PHD3 can only hydroxylate the Pro-564 position.

Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ PHD2]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (as mentioned above) in [http://en.wikipedia.org/wiki/HIF1A HIF-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref> Our goal in the Knapp Lab is to understand and define the mechanism of action for this enzyme and evaluate how oxygen affects enzyme activity to improve knowledge of oxygen sensing.

<structure load='2g19' size='335' frame='true' align='right'
caption='Significant structural features of Prolyl Hydroxylase Domain-2 (PHD-2) enzyme [[2g19]] and 3HQR' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain 2 (PHD2) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions such as Fenton chemistry.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 (shown in purple) undergoes a large <scene name='60/609795/B2b3_loop_with_cood/1'>conformational change</scene>. The β2β3 loop moves toward the active site and closes over the active site entrance. This loop movement is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. Hydroxylation occurs within the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A HIF-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of HIF-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results in degradation of HIF-α by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A HIF-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-12-03T19:25:12Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

These HIF-hydroxylase enzymes include the Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both. <ref>PMID:12615973</ref> This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" /> PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates either the Pro-402 or Pro-564 residue in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A HIF-α] whereas PHD3 can only hydroxylate the Pro-564 position.

Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ PHD2]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (as mentioned above) in [http://en.wikipedia.org/wiki/HIF1A HIF-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref> Our goal in the Knapp Lab is to understand and define the mechanism of action for this enzyme and evaluate how oxygen affects enzyme activity to improve knowledge of oxygen sensing.

<structure load='2g19' size='335' frame='true' align='right'
caption='Significant structural features of Prolyl Hydroxylase Domain-2 (PHD-2) enzyme [[2g19]] and 3HQR' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain 2 (PHD2) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions such as Fenton chemistry.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 undergoes a large <scene name='60/609795/B2b3_loop_with_cood/1'>conformational change</scene> (Figure 1). The β2β3 loop moves toward the active site and closes over the active site entrance. This loop movement is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. Hydroxylation occurs within the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A HIF-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of HIF-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results in degradation of HIF-α by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A HIF-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-12-03T19:21:21Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

These HIF-hydroxylase enzymes include the Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both. <ref>PMID:12615973</ref> This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" /> PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates either the Pro-402 or Pro-564 residue in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A HIF-α] whereas PHD3 can only hydroxylate the Pro-564 position.

Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ PHD2]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (as mentioned above) in [http://en.wikipedia.org/wiki/HIF1A HIF-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref> Our goal in the Knapp Lab is to understand and define the mechanism of action for this enzyme and evaluate how oxygen affects enzyme activity to improve knowledge of oxygen sensing.

<structure load='2g19' size='335' frame='true' align='right'
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain 2 (PHD2) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions such as Fenton chemistry.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 undergoes a large <scene name='60/609795/B2b3_loop_with_cood/1'>conformational change</scene> (Figure 1). The β2β3 loop moves toward the active site and closes over the active site entrance. This loop movement is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

[[Image:PHD2.png|315 px|thumb|Fig. 1: Substrate bound (purple) and unbound (green) PHD2. Figure created with PyMol. PDB IDs 2G19, 3HQR.]]

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. Hydroxylation occurs within the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A HIF-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of HIF-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results in degradation of HIF-α by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A HIF-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-11-21T20:41:50Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

These HIF-hydroxylase enzymes include the Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both. <ref>PMID:12615973</ref> This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" /> PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates either the Pro-402 or Pro-564 residue in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A HIF-α] whereas PHD3 can only hydroxylate the Pro-564 position.

Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ PHD2]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (as mentioned above) in [http://en.wikipedia.org/wiki/HIF1A HIF-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref> Our goal in the Knapp Lab is to understand and define the mechanism of action for this enzyme and evaluate how oxygen affects enzyme activity to improve knowledge of oxygen sensing.

<structure load='2g19' size='335' frame='true' align='right'
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain 2 (PHD2) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions such as Fenton chemistry.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 undergoes a large conformational change (Figure 1). The β2β3 loop moves toward the active site and closes over the active site entrance. This loop movement is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

[[Image:PHD2.png|315 px|thumb|Fig. 1: Substrate bound (purple) and unbound (green) PHD2. Figure created with PyMol. PDB IDs 2G19, 3HQR.]]

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. Hydroxylation occurs within the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A HIF-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of HIF-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results in degradation of HIF-α by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A HIF-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-11-21T20:21:20Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

These HIF-hydroxylase enzymes include the Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both. <ref>PMID:12615973</ref> This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" /> PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates either the Pro-402 or Pro-564 residue in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] whereas PHD3 can only hydroxylate the Pro-564 position.

Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ (PHD2)]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (as mentioned above) in [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref> Our goal in the Knapp Lab is to understand and define the mechanism of action for this enzyme and evaluate how oxygen affects enzyme activity to gaining further knowledge of oxygen sensing.

<structure load='2g19' size='335' frame='true' align='right'
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain (PHD) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions like the Fenton type reaction.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 goes through a large conformational change (Figure 1). The β2β3 loop moves toward the active site and closes the active site entrance and it is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

[[Image:PHD2.png|315 px|thumb|Fig. 1: Substrate bound (purple) and unbound (green) PHD2. Figure created with PyMol. PDB IDs 2G19, 3HQR.]]

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. The hydroxylation happens in the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of (HIF)-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results to degradation by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-11-21T19:45:23Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

These HIF-hydroxylase enzymes include Prolyl Hydroxylase Domain isoforms (PHDs) and Factor Inhibition Hypoxia Inducible Factor (FIH). PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, while PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both <ref>PMID:12615973</ref>.This distribution contrasts with that of the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally included three [http://en.wiktionary.org/wiki/homolog homolog] members: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]). Recently, a newly identified enzyme called P4H-TM (also named PHD4 and EGLN4) was added to this subfamily. Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" />. PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates Pro-402 or Pro-564 residues in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] whereas PHD3 can only hydroxylate the Pro-564 position.

Of the HIF-hydroxylases, '''[http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ (PHD2)]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (in humans, Pro-402 and Pro-564) in [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref>

<structure load='2g19' size='335' frame='true' align='right'
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain (PHD) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions like the Fenton type reaction.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 goes through a large conformational change (Figure 1). The β2β3 loop moves toward the active site and closes the active site entrance and it is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

[[Image:PHD2.png|315 px|thumb|Fig. 1: Substrate bound (purple) and unbound (green) PHD2. Figure created with PyMol. PDB IDs 2G19, 3HQR.]]

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. The hydroxylation happens in the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of (HIF)-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results to degradation by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-11-21T19:35:47Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

Of the HIF-hydroxylases, '''Prolyl hydroxylase domain [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ (PHD)]''' is believed to be the main oxygen sensor. PHD2 is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (in humans, Pro-402 and Pro-564) in [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref>

PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both <ref>PMID:12615973</ref> in contrast to [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally includes three [http://en.wiktionary.org/wiki/homolog homolog] members but was recently updated to include another member: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]), and a newly identified enzyme called P4H-TM (also recently named PHD4 and EGLN4). Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" />. PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates Pro-402 and Pro-564 residues in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] whereas PHD3 can only hydroxylate Pro-564 position.

<structure load='2g19' size='335' frame='true' align='right'
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain (PHD) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions like the Fenton type reaction.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 goes through a large conformational change (Figure 1). The β2β3 loop moves toward the active site and closes the active site entrance and it is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

[[Image:PHD2.png|315 px|thumb|Fig. 1: Substrate bound (purple) and unbound (green) PHD2. Figure created with PyMol. PDB IDs 2G19, 3HQR.]]

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. The hydroxylation happens in the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of (HIF)-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results to degradation by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-11-21T19:32:07Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] by the HIF-hydroxylase enzymes, which are studied extensively by the [http://people.chem.umass.edu/knapplab/?q=knappchem/index.html Knapp Lab] here at UMass Amherst.<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

'''Prolyl hydroxylase domain (PHD) enzyme''' [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ (EC 1.14.11.-)] is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (in humans, Pro-402 and Pro-564) in [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref>

PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both <ref>PMID:12615973</ref> in contrast to [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally includes three [http://en.wiktionary.org/wiki/homolog homolog] members but was recently updated to include another member: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]), and a newly identified enzyme called P4H-TM (also recently named PHD4 and EGLN4). Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" />. PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates Pro-402 and Pro-564 residues in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] whereas PHD3 can only hydroxylate Pro-564 position.

<structure load='2g19' size='335' frame='true' align='right'
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain (PHD) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions like the Fenton type reaction.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 goes through a large conformational change (Figure 1). The β2β3 loop moves toward the active site and closes the active site entrance and it is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

[[Image:PHD2.png|315 px|thumb|Fig. 1: Substrate bound (purple) and unbound (green) PHD2. Figure created with PyMol. PDB IDs 2G19, 3HQR.]]

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. The hydroxylation happens in the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of (HIF)-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results to degradation by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-11-19T18:01:36Z

Vanessa Chaplin:

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation of specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

'''Prolyl hydroxylase domain (PHD) enzyme''' [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ (EC 1.14.11.-)] is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of specific proline residues (in humans, Pro-402 and Pro-564) in [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref>

PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both <ref>PMID:12615973</ref> in contrast to [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally includes three [http://en.wiktionary.org/wiki/homolog homolog] members but was recently updated to include another member: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]), and a newly identified enzyme called P4H-TM (also recently named PHD4 and EGLN4). Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" />. PHDs differ in terms of the proline hydroxylation site. PHD2 hydroxylates Pro-402 and Pro-564 residues in the oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] whereas PHD3 can only hydroxylate Pro-564 position.

<structure load='2g19' size='335' frame='true' align='right'
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 in complex with hydroxy-iodoisoquinolin-carbonyl glycine (HG) [[2g19]]' />

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain (PHD) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='40/400587/Molecular_playground/5'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases.

The <scene name='40/400587/Active_site/8'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the three Fe(II)-binding <scene name='40/400587/Active_site/14'>ligands</scene> formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" /> , 2-OG (which in this scene is replaced by HG) and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions like the Fenton type reaction.<ref name="structure" />

Upon binding of substrate, the <scene name='40/400587/B2b3_loop/2'>β2β3</scene> loop region of PHD2 goes through a large conformational change (Figure 1). The β2β3 loop moves toward the active site and closes the active site entrance and it is believed to be essential for the catalytic function of PHD2. The β2β3 loop region is mostly conserved in PHDs with minor differences. Mutational studies on the β2β3 loop region showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

[[Image:PHD2.png|315 px|thumb|Fig. 1: Substrate bound (purple) and unbound (green) PHD2. Figure created with PyMol. PDB IDs 2G19, 3HQR.]]

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. The hydroxylation happens in the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review" />
Proline hydroxylation in NODD and CODD enable recognition of (HIF)-α by the von Hippel Lindau (pVHL) ubiquitin ligase complex which ultimately results to degradation by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Vanessa Chaplin/sandbox2

2014-11-19T17:34:12Z

Vanessa Chaplin: New page: ==Your Heading Here (maybe something like 'Structure')== <StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''> This is a default text for you...

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
This is a default text for your page '''Vanessa Chaplin/sandbox2'''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

== Function ==

== Disease ==

== Relevance ==

== Structural highlights ==

== Headline text ==

This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

</StructureSection>
== References ==
<references/>

CBI Molecules

2013-12-04T02:32:51Z

Vanessa Chaplin: /* Molecules */

These are molecules under study by members of the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program].
Many of the molecules we study are featured at the [http://www.molecularplayground.org/ Molecular Playground] (see also [[Molecular Playground|Molecular Playground in Proteopedia]]). Follow the links below to read nontechnical descriptions, in Proteopedia, of these molecules.

UMass CBI Members, add your molecules to the list (which is alphabetical by CBI research mentor); follow the instructions below the list.

Fall 2013: CBI Molecules are due 12/4/13 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished, and then as "New 2013" or "Revised 2013". For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed (or include credits to the original page and authors if it does not).

==Molecules==
'''** Designates CBI Molecules Featured on [http://http://www.umass.edu/cbi/ CBI website]'''

Bhatia Lab

: '''[[Molecular Playground/Alginate-Fall2011]]''', Joe White, David Griffin

: '''[[Molecular Playground/Alginate-Fall2010]]''', Joe White, David Griffin

: '''[[Molecular Playground/Poly(ethylene glycol)]]''', Erika M. Saffer

[http://chamberslab.com/wp/ Chambers Lab]

: '''[[Molecular Playground/Glutamate Receptor]]''', Amanda Hussey, Steve McCarron, Rosie Combs-Bachmann, Mariel Feliciano

[http://www.chem.umass.edu/~chenlab/index.HTML Chen Lab]

: New Fall 2012!! '''[[Molecular Playground/OmpG]]''', Christina Chisholm

[http://openwetware.org/wiki/Chien Chien Lab]

New Fall 2013! : **'''[[Molecular Playground/Homo-dimeric RcdA]]''', Kamal K. Joshi

: **'''[[Molecular Playground/Hexameric ClpX]]''', Joanne Lau
:: Best CBI Molecule 2011

: '''[[Molecular Playground/DNA replication initiator DnaA]]''', Jing Liu

Forbes Lab

: '''[[Molecular Playground/CheR]]''', Miaomin Zhang

: '''[[Molecular Playground/RBP]]''', Jan Panteli

: '''[[Molecular Playground/TRAIL]]''', Charley Swofford

[http://www.biochem.umass.edu/garman/index.html Garman Lab]

: '''[[Molecular Playground/Human Protective Protein Cathepsin A]]''', Yadilette Rivera-Colon

: '''[[Molecular Playground/Human PPCA]]''', Nilima Kolli

[http://people.chem.umass.edu/gieraschlab/ Gierasch Lab]

: '''[[CRABP I ( Cellular Retinoic Acid Binding Protein )|Molecular Playground/CRABP I]]''', Kristine Faye Pobre, Mylene Ferrolino,Mangai Periasamy
:: Best Overall CBI Molecule 2010

: '''[[Molecular Playground/CRABP I (Cellular Retinoic Acid Binding Protein)]]''', Gustavo Elberto Epalza Sanchez
(compare this to the previous version above to see what's new)

: **'''[[Molecular_Playground/DHFR]]''', Karan Hingorani
:: Best CBI Molecule 2012

[http://people.chem.umass.edu/jhardy/ Hardy Lab]

: New Fall 2013!! '''[[Molecular Playground/Executioner Caspase-7]]''', Derek MacPherson, Maureen E. Hill

: '''[[Molecular Playground/[[Caspase-3 Regulatory Mechanisms]]''', Scott Eron, Bay Serrano, Yunlong Zhao

: ''' [[Molecular Playground/Caspase-6 and neurodegeneration]]''', Kevin Buadlart Dagbay

: '''[[Molecular Playground/Caspase-7 Dynamics]]'''

: '''[[Molecular Playground/Caspase-9 Regulation]]''', Kristen Huber

: '''[[Molecular Playground/Caspase-6 (new)]]''', Elih Velazquez

: '''[[Molecular Playground/Influenza A M2 transmembrane domain]]''', Samantha Nicholls

: '''[[Molecular Playground/Dengue Virus Protease]]''', Muslum Yildiz

Hebert Lab

: New Fall 2012!! '''[[Molecular_Playground/ERDj5]]''', Lydia Lamriben
: '''[[Molecular Playground/Saposin C]]''', Abla Tannous
: '''[[Molecular_Playground/ERMan1]]''', Johan Sunryd

[http://people.biochem.umass.edu/aheuck/aph.html Heuck Lab]

: Updated Fall 2012!! '''[[Molecular_Playground/Pcr H]]''', Fabian Romano, Carolina Morell-Pérez

[http://people.chem.umass.edu/mholden/ Holden Lab]

: New Fall 2012!! '''[[Molecular Playground/Protective Antigen]]''', Jing Huang

[http://www.chem.umass.edu/people/kaltashovlab/ Kaltashov Lab]

: Updated Fall 2012!! ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin, Jake Pawlowski

: '''[[Molecular Playground/Velaglucerase]]''', Adriana Kita

Knapp lab

: Updated Fall 2013!! '''[[Molecular Playground/FIH]]''', Vanessa Chaplin, Cornelius Taabazuing, Breanne Holmes, John Hangasky

: Updated Fall 2012!! '''[[Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme]]''', Cristina Martin, Serap Pektas
:: Best CBI Molecule Proteopedia Page 2010

[http://people.chem.umass.edu/mmaroney/ Maroney Lab]

: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: Updated Fall 2013!! '''[[Molecular Playground/CsoR and RcnR]]''', Heidi Hu, Carolyn Carr
: '''[[Molecular Playground/HypA]]''', Heidi Hu

[http://www.chem.umass.edu/~cmartin/ Martin Lab]

: **'''[[Molecular Playground/T7 RNAP Conformations]]''', Luis E. Ramirez-Tapia
:: Best CBI Molecule 2011
: '''[[Molecular Playground/T7 RNA Polymerase (7 mer int)]]''', Ankit Vahia

: '''[[Molecular Playground/Human mtRNA pol]]''', Ketan Mathavan

[http://www.peytonlab.org/ Peyton Lab]
: '''[[Molecular Playground/C-Raf]]''', Thuy Nguyen
: '''[[Molecular Playground/FAK]]''', Dannielle Ryman
: New Fall 2013! '''[[Molecular Playground/MMP14]]''', Lauren Jansen

[http://roberts.openwetware.org/ Roberts Lab]

: '''[[Molecular Playground/Taxol]]''', Rohan Patil, Sarah Wilson

: '''[[Molecular Playground/Insulin]]''', Whitney Stoppel

[http://www.umass.edu/rotellogroup/ Rotello Lab]

: '''[[Reverse transcriptase|Molecular Playground/Reverse Transcriptase]]''', Daniel Moyano-Marino

: '''[[Molecular Playground/Pancreatic Lipase]]''', Rui Tang

: '''[[Molecular playground/Chymotrypsin]]''', Brad

: '''[[Molecular Playground/Targeting Peptide]]''', David Solfiell

[http://http://www.umass.edu/schiffman/ Schiffman Lab]
:New Fall 2013! '''[[Molecular Playground/Streptavidin]]''', Katrina Rieger

[https://elements.chem.umass.edu/schnarrlab/ Schnarr Lab]

: New Fall 2012!! '''[[Molecular Playground/4'-PHOSPHOPANTETHEINYL TRANSFERASE (Sfp)]]''', Jon Amoroso, Gitanjeli Prasad, Lawrence Sheringham Borketey

: '''[[6-deoxyerythronolide_B_synthase_(DEBS)|Molecular Playground/6-Deoxyerythronolide B Synthase]]''', Tsung-Yi Lin, Jon Amoroso, Lawrence Sheringham Borketey

: '''[[Molecular Playground/ACP apo]]''', Gitanjeli Prasad

[http://www.biochem.umass.edu/faculty/danny-j-schnell Schnell Lab]
: New Fall 2012!! '''[[Molecular Playground/Tic40]]''', Mine Canakci

Tew Lab

: '''[[Molecular Playground/HIV Tat]]''', Brittany deRonde

Thayumanavan Lab

: '''[[Molecular Playground/Lysozyme ]]''', Daniella Gonzalez

: '''[[Molecular Playground/Beta-galactosidase]]''', Judy Ventura

: '''[[User:Krishna Reddy Ragupathi|Molecular Playground/Carbonic Anhydrase]]''', Krishna Reddy Raghupathi

: '''[[User:Rami Rajasekhar Reddy|Molecular Playground/Avidin]]''', Rami Rajasekar Reddy

: '''[[Molecular Playground/Biotin binding avidin]]''', Diego Amado

: '''[[User:Jiaming Zhuang|Molecular Playground/MMP12]]''', Jiaming Zhuang

: ''' [[User:Jing Guo|Molecular Playground/Gluconase]]''', Jing Guo

: '''[[Molecular Playground/Glutathione Reductase]]''', Reuben Chacko

Thayumanavan & Vachet Labs

: '''[[Molecular Playground/Trypsin]]''', Gladys Murage

[http://people.chem.umass.edu/thompson/index.html Thompson] & [http://www.chem.umass.edu/~rmweis/weislab/ Weis] Labs

: New Fall 2012!! '''[[Molecular Playground/CheA]]''', Elizabeth R. Haglin

: '''[[Molecular Playground/Bacterial Chemotaxis Receptors]]''', Lynmarie K. Thompson, Shiela M. Jones

: '''[[Molecular Playground/cytoplasmic domain of a serine chemotaxis receptor]]''', Meili Yang

: '''[[Molecular Playground/Cytoplasmic domain of chemoreceptor of Thermotoga maritima]]''', Xuni Li

[http://www.chem.umass.edu/~vachet/index.html Vachet Lab]

: '''[[Molecular playground/beta 2 microglobulin]]''', Nick Borotto
:: Best CBI Molecule Jmol scenes 2010

: '''[[Molecular Playground/Myoglobin]]''', Yuping Zhou

:'''[[Molecular Playground/ Copper-Zinc Superoxide Dismutase]]''', Shaynah Browne

: New Fall 2012!! '''[[Molecular Playground/Ubiquitin salt bridge discussion]]''', Zhe Zhang

Other Molecules of interest

: '''[[Molecular Playground/PcrA Helicase]]''', Luis E Ramirez-Tapia, [http://www.chem.umass.edu/~cmartin/ Martin Lab]

Other Laboratories

: '''[[Molecular Playground/YKL-40]]''', Ralph A. Francescone III, [http://www.bio.umass.edu/mcb/faculty/Shao.html Shao Lab]

: '''[[Molecular Playground/BLG|Molecular Playground/β-lactoglobulin]]''', Daniel Seeman, Dubin Lab

: '''[[Molecular Playground/ADAM13]]''', Genevieve Abbruzzese, Alfandari Lab

==Instructions==

'''The goal is for students to work collaboratively to create one excellent CBI Molecule for each CBI research group, to be featured on the CBI website.'''

Fall 2013: Complete steps 1-2 by 10/18, and bring your computer to the CBI Molecule Workshop on Wed 10/23 in ISB 321.

A successful CBI Molecule will be an interesting, nontechnical description of a molecule related to your group's research. It should not be super long, but instead have multiple green scenes. Green scenes should clearly show an interesting feature and should be attractive. Use the green scenes to help you make interesting points about the molecule (do not try to describe every feature of the molecule). It's great if you can end with a brief statement about how it relates to your group's research goals.

1. If you don't already have one, request a Proteopedia account and log in.

2. Read through the rest of the instructions and look at any existing CBI Molecules from your research group. Talk with other Chalk Talk students in your research group and think about how you can make a new or improved CBI Molecule related to your group's research. Develop ideas for the scenes you wish to show. You will work learn how to make scenes during the workshop.

3. Get started working in Proteopedia by using the links at [[Help:Contents]]. Make yourself a sandbox page: Enter "User:Your Name/Sandbox 1" (omit quotes) in the search box, then follow instructions to edit this page. Practice entering text, inserting a structure window with scrolling text (green 4-square button on the right), and creating a green scene. You can look at other Proteopedia pages in edit mode to see how different effects (like colored text) are achieved (but this won't show you how the scene effects are made).

4. For those editing an existing CBI Molecule, start from that entry so that it retains the full author list of all authors that contributed. You are encouraged to collaborate on the CBI Molecules, but everyone will need to do some editing of the molecule so that they each appear as authors on the final list. If you are the sole student from your group enrolled in Chalk Talk and have not previously made a CBI Molecule, try to convince another group member who has previously made a CBI Molecule (see list above) to join us for the workshop so that you can work together.

5. Your final pages should be called "Molecular Playground/your molecule" and should have links on this CBI Molecule page -- put the new ones first on the list from your research group. Label them "in progress" until you are finished, and then "new 2013" or "revised 2013".

==Links to HELP pages==
Overview at [[Help:Contents ]]

See also [[Help:Getting_Started_in_Proteopedia]]

Videos showing how to use Proteopedia:
[[Proteopedia:Video_Guide]]
(Sometimes slow -- if you pause the video and wait awhile it will download and then you can play it without interruptions)

[[Proteopedia:DIY:Scenes|Proteopedia Scenes: Do It Yourself]]
gives succinct step by step instructions on how to create a molecular scene.

A powerpoint-like set of slides that walks a user through the process of creating a new page and a new molecular scene/green link.
[http://www.proteopedia.org/wiki/images/1/1b/2009_07_13_Proteopedia_Workshop.pdf Proteopedia Workshop Slides]

[[Proteopedia:Guidelines for Ethical Writing]].
Please pay attention to the section about images. There are links to examples of images re-used with explicit permission.

For other help resources, click on [[Help:Contents|Help]] in the ''navigation'' box at the upper left of every page in Proteopedia.

Molecular Playground/FIH

2013-12-04T02:29:22Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue
(<scene name='40/400574/Asn803/1'>Asn803</scene>) in the C-Terminal Trans-Activation Domain (CTAD) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='40/400574/Active_site/1'>FIH active site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown. <scene name='40/400574/Conservation/1'>Here</scene> we see that the β-barrel core of the enzyme is highly conserved whereas the α-helices on the surface maintain variability.

=== Solvent Isotope Effects ===

Studies show that Solvent Isotope Effects (SIEs) can probe water release from metals given that the water release occurs prior to the rate limiting step of the reaction. SIEs conducted on FIH revealed an inverse SIE based on ''kcat'' and ''kcat/Km'' values indicating the rate of the reaction in D2O is greater than the reaction rate in H2O. These results conclude that the rate limiting step in the FIH reaction pathway is O2 activation.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T02:28:56Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue
(<scene name='40/400574/Asn803/1'>Asn803</scene>) in the C-Terminal Trans-Activation Domain (CTAD) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='40/400574/Active_site/1'>FIH active site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown. <scene name='40/400574/Conservation/1'>Here</scene> we see that the β-barrel core of the enzyme is highly conserved whereas the α-helices on the surface maintain variability.

=== Solvent Isotopes Effects ===

Studies show that Solvent Isotope Effects (SIEs) can probe water release from metals given that the water release occurs prior to the rate limiting step of the reaction. SIEs conducted on FIH revealed an inverse SIE based on ''kcat'' and ''kcat/Km'' values indicating the rate of the reaction in D2O is greater than the reaction rate in H2O. These results conclude that the rate limiting step in the FIH reaction pathway is O2 activation.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T02:25:56Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue
(<scene name='40/400574/Asn803/1'>Asn803</scene>) in the C-Terminal Trans-Activation Domain (CTAD) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='40/400574/Active_site/1'>FIH active site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown. <scene name='40/400574/Conservation/1'>Here</scene> we see that the β-barrel core of the enzyme is highly conserved whereas the α-helices on the surface maintain variability.

=== Solvent Isotopes Effects ===

Studies show that Solvent Isotope Effects (SIEs) can probe water release from metals given that the water release occurs prior to the rate limiting step of the reaction. SIEs conducted on FIH revealed an inverse SIE based on ''kcat'' and ''kcat/Km'' values indicating the rate of the reaction in D2O is greater than the reaction rate in H2O. These results conclude that the rate limiting step in the FIH reaction pathway is O2 activation.

[[Image:consensus mechanism.png]]

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T01:31:28Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue
(<scene name='40/400574/Asn803/1'>Asn803</scene>) in the C-Terminal Trans-Activation Domain (CTAD) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='40/400574/Active_site/1'>FIH active site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown. <scene name='40/400574/Conservation/1'>Here</scene> we see that the β-barrel core of the enzyme is highly conserved whereas the α-helices on the surface maintain variability.

=== Solvent Isotopes Effects ===

Studies show that Solvent Isotope Effects (SIEs) can probe water release from metals given that the water release occurs prior to the rate limiting step of the reaction. SIEs conducted on FIH revealed an inverse SIE based on ''kcat'' and ''kcat/Km'' values indicating the rate of the reaction in D2O is greater than the reaction rate in H2O. These results conclude that the rate limiting step in the FIH reaction pathway is O2 activation.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T01:10:31Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue
(<scene name='40/400574/Asn803/1'>Asn803</scene>) in the C-Terminal Trans-Activation Domain (CTAD) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='40/400574/Active_site/1'>FIH active site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown. <scene name='40/400574/Conservation/1'>Here</scene> we see that the β-barrel core of the enzyme is highly conserved whereas the α-helices on the surface maintain variability.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T00:58:12Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue
(<scene name='40/400574/Asn803/1'>Asn803</scene>) in the C-Terminal Trans-Activation Domain (CTAD) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='40/400574/Active_site/1'>FIH active site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T00:55:21Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue
(<scene name='40/400574/Asn803/1'>Asn803</scene>) in the C-Terminal Trans-Activation Domain (CTAD) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T00:43:48Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (CTAD) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T00:27:32Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. <scene name='40/400574/Hif/3'>HIF</scene> consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T00:05:57Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-04T00:04:33Z

Vanessa Chaplin:

<Structure load='1H2L' size='300' frame='true' align='right' caption='FIH in complex with HIF, Fe+2, and α-KG' scene='<scene name='40/400574/Fih/1'>TextToBeDisplayed</scene>' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-03T23:58:52Z

Vanessa Chaplin:

<Structure load='FIH_overall_structure' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-03T23:57:40Z

Vanessa Chaplin:

<Structure load='<scene name='40/400574/Fih_overall_structure/1'>TextToBeDisplayed</scene>' size='300' frame='true' align='right' caption='Human FIH complex with HIF, Fe+2, sulfate, and α-KG [[1H2L]]' scene='' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-03T23:10:44Z

Vanessa Chaplin:

<Structure load='1h2l' size='300' frame='true' align='right' caption='Human FIH complex with HIF, Fe+2, sulfate, and α-KG [[1H2L]]' scene='' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-03T23:02:08Z

Vanessa Chaplin:

<Structure load='1h2l' size='300' frame='true' align='right' caption='Human FIH complex with HIF, Fe+2, sulfate, and αKG [[1h2l]]' scene='' />

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

File:1H2L (2).pdb

2013-12-03T23:01:27Z

Vanessa Chaplin: 1H2L Crystal Structure

== Summary ==
1H2L Crystal Structure
== Licensing ==
{{subst:No license from license selector|Don't know}}

Molecular Playground/FIH

2013-12-03T22:58:24Z

Vanessa Chaplin:

<Structure load='1h2l' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' /> CAPTION=Human FIH complex with HIF, Fe+2, sulfate and 2-oxoglutaric acid, [[1h2l]] }}

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/FIH

2013-12-03T22:28:07Z

Vanessa Chaplin:

{{STRUCTURE_1h2l| PDB=1h2l | SIZE=300| SCENE=User:John_Hangasky/Sandbox_1/Fih/4|right| CAPTION=Human FIH complex with HIF, Fe+2, sulfate and 2-oxoglutaric acid, [[1h2l]] }}

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

<Structure load='1h2l' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme

2013-11-30T18:51:20Z

Vanessa Chaplin:

<structure load='2g19' size='350' frame='true' align='left'
caption='Prolyl Hydroxylase Domain-2 (PHD-2) enzyme with Fe+2 complex with hydroxy-iodoisoquinolin-carbonyl glycine [[2g19]]' />

One of the [[CBI Molecules]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

=== Introduction ===

Metazoans adapt to oxygen levels in the environment by making use of intracellular oxygen levels as signals to regulate the [http://en.wikipedia.org/wiki/Transcription_(genetics) transcription] of genes that are essential under normoxic or [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxic] conditions. Central to this mechanism is the oxygen-dependent hydroxylation on specific proline and asparagine residues of the transcription factor, hypoxia-inducible factor [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review">Fong, G.H., Takeda, K. "Role and Regulation of Prolyl Hydroxylase Domain Proteins." Cell Death and Differentiation, February 15, 2008, 15, 635-641. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18259202 18259202]</ref>

'''Prolyl hydroxylase domain (PHD) enzyme''' [http://www.chem.qmul.ac.uk/iubmb/enzyme/EC1/14/11/ (EC 1.14.11.-)] is a Fe(II)/2-oxoglutarate (OG)-dependent [http://en.wikipedia.org/wiki/Oxygenase dioxygenase] that catalyzes the ''trans''-4-hydroxylation of the specific proline residues (in humans, Pro-402 and Pro-564) in [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]. In addition to iron, this enzyme also requires [http://en.wikipedia.org/wiki/Vitamin_C ascorbate] as a cofactor.<ref name="structure">Mcdonough, M.A., Li, V., Flashman, E., et al. "Cellular oxygen sensing: Crystal structure of hypoxia-inducible factor prolyl hydroxylase (PHD2)." PNAS, June 27, 2006, 103 (26), 9814-9819. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16782814 16782814]</ref>

PHDs belong to the same oxygenase superfamily as the [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases. Inside the cell, PHD1 is found in the nucleus, PHD2 is mostly located in the cytoplasm and PHD3 is distributed in both <ref>PMID:12615973</ref> in contrast to [http://en.wikipedia.org/wiki/Collagen collagen] prolyl hydroxylases, which reside in the endoplasmic reticulum. In mammals, the PHD dioxygenase subfamily originally includes three [http://en.wiktionary.org/wiki/homolog homolog] members but was recently updated to include another member: PHD1 (also known as HPH3 and [http://en.wikipedia.org/wiki/EGLN2 EGLN2]), PHD2 (also known as HPH2 and [http://en.wikipedia.org/wiki/EGLN1 EGLN1]), PHD3 (also known as HPH1 and [http://en.wikipedia.org/wiki/EGLN3 EGLN3]), and a newly identified enzyme called P4H-TM (also recently named PHD4 and EGLN4). Both PHD1 and PHD2 contain more than 400 [http://en.wikipedia.org/wiki/Amino_acid amino acid] residues while PHD3 has less than 250. All isoforms, however, contain the highly conserved hydroxylase domain in the catalytic carboxy-terminal region. <ref name="review" />. PHDs differ in terms of the proline hydroxylation, PHD2 hydroxylates Pro-402 and Pro-564 residue in oxygen degradation domain of [http://en.wikipedia.org/wiki/HIF1A (HIF)-α] whereas PHD3 can only hydroxylate Pro-564 position.

<scene name='Molecular_Playground/Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Molecular_playground/4'>Molecular Playground</scene>

Molecular Playground banner: Prolyl Hydroxylase Domain (PHD) enzyme, a cellular oxygen sensor, has a major regulatory role in oxygen homeostasis.

=== Structure ===
----
[[Image:PHD2.png|300 px|thumb|Fig. 1: Substrate bound (purple) and unbound (green) PHD2. Figure created with PyMol. PDB IDs 2G19, 3HQR.]]

PHDs have two structural domains: the more variable N-terminal domain and the conserved catalytic C-terminal domain. The catalytic domain core of PHDs consists of eight β-strands in a "jelly-roll" or double stranded β helix <scene name='Sandbox_Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Jelly_roll_fold/3'>(DSBH) fold motif</scene> supported by three conserved α-helices and other β-strands and loops that pack along the core. Possession of the DSBH motif is typical of 2-OG-dependent oxygenases. Contained in this core are the three Fe(II)-binding ligands formed by the conserved triad sequence, His-X-Asp/Glu-Xn-His.<ref name="review" /><ref>Schofield, C.J., Ratcliffe, P.J. "Signalling Bypoxia by HIF Hydroxylases." Biochemical and Biophysical Research Communications, August 24, 2005, 338, 617-626. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16139242 16139242]</ref><ref name="structure" />

The <scene name='Sandbox_Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Active_site/2'>active site</scene>, which is located on a deep cleft between the β-strands comprising the DBSH core, contains the essential Fe(II). It is normally coordinated by the conserved two-histidine-one-carboxylate <scene name='Sandbox_Prolyl_Hydroxylase_Domain_(PHD)_Enzyme/Fe_binding_triad_sequence/2'>triad</scene>, 2-OG and a water molecule to form an octahedral geometry. Aside from the triad motif residues and those that bind 2-OG, the residues that are predominant inside the active site are nonpolar in nature. This is evidence of the enzyme's need to protect the protein core from oxidation by reactive species that are sometimes generated from iron-related reactions like the Fenton type reaction.<ref name="structure" />

Upon binding of substrate β2β3 loop region of PHD2 goes to a large conformational change (Figure 1). β2β3 loop moves toward the active site and closes the active site entrance and it is believed to be essential for catalytic function of PHD2. β2β3 loop region is mostly conserved in PHDs with some differences. Mutational studies on β2β3 loop region has showed that this loop is significant for substrate recognition of PHDs<ref>PMID:18063574</ref>.

=== Function ===
----
The intrinsic dependence of PHD-catalyzed hydroxylation reactions on molecular oxygen concentration led to the most notable role of PHDs as cellular oxygen sensors. The hydroxylation happens in the oxygen degradation domain at position 4 of the residues Pro-402 (NODD) and Pro-564 (CODD) of [http://en.wikipedia.org/wiki/Hypoxia_(medical) hypoxia]-inducible transcription factor, [http://en.wikipedia.org/wiki/HIF1A (HIF)-α].<ref name="review" />
Proline hydroxylation in NODD and CODD, enable recognition by the von Hippel Lindau (pVHL) ubiquitin ligase complex and flowing degradation by the proteasome<ref>PMID:11292862</ref> <ref>PMID:11292861</ref>.

The requirement of PHDs for the [http://en.wikipedia.org/wiki/Citric_acid_cycle TCA cycle] intermediate, 2-oxoglutarate, also opens the possibility of these enzymes acting as regulators of processes that relate metabolic activity to oxygen levels. Aside from regulation of oxygen homeostasis, other biological functions of the enzyme, which may be hydroxylase-independent or still hydroxylase-dependent but [http://en.wikipedia.org/wiki/HIF1A (HIF)-α]-independent, are being proposed. This is mainly based on the results of various studies: some showed that other factors such as [http://en.wikipedia.org/wiki/Nitric_oxide nitric oxide], [http://en.wikipedia.org/wiki/Reactive_oxygen_species reactive oxygen species] (ROS), and several [http://en.wikipedia.org/wiki/Oncogene oncogenes] control PHD oxygenase activity<ref>Kaelin, W.G. "Proline Hydroxylation and Gene Expression." Annu.Rev.Biochem., February 8, 2005, 74, 115-128. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15952883 15952883]</ref>; while others described PHD activity on other substrates like [http://en.wikipedia.org/wiki/IKK2 IKK-β]<ref name="review" />. In fact, several functions of the enzyme have been recently identified based on these studies. Listed below are the currently identified functions for PHDs in general<ref name="review" />:
*tumor suppressor
*promoter of cell death ([http://en.wikipedia.org/wiki/Apoptosis apoptosis])
*regulator of cell differentiation

=== Substrate Preference ===

===3D structures of hypoxia-inducible factor prolyl hydroxylase ===

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
----
<references/>

Molecular Playground/FIH

2013-11-26T21:48:11Z

Vanessa Chaplin:

{{STRUCTURE_1h2l| PDB=1h2l | SIZE=300| SCENE=User:John_Hangasky/Sandbox_1/Fih/4|right| CAPTION=Human FIH complex with HIF, Fe+2, sulfate and 2-oxoglutaric acid, [[1h2l]] }}

=== Factor Inhibiting HIF ===

'''H'''ypoxia '''I'''nducible '''F'''actor (HIF)is a heterodimeric transcription factor that regulates over 100 genes. HIF consists of a constitutively expressed beta subunit, and an alpha subunit that is regulated in oxygen dependent manner. There are two enzymes that regulate HIF controlled gene expression, '''F'''actor '''I'''nhibiting '''H'''IF (FIH) and '''P'''rolyl '''H'''ydroxylase '''D'''omain 2 (PHD2). Under normoxic conditions, hydroxylation of one or both proline residues in the Oxygen Degradation Domain (ODD) of HIF results in proteosomal degradation of the HIF alpha subunit. Hydroxylation of an asparagine residue in the C-Terminal Trans-Activation Domain (<scene name='User:John_Hangasky/Sandbox_1/Fih/5'>CTAD</scene>) of HIF by FIH results in transcriptional silencing of genes due to HIF's inability to recruit the co-activator p300. However, under hypoxic conditions, there is no hydroxylation, resulting in stabilization of the HIF alpha subunit. The alpha subunit dimerizes with the beta subunit and HIF is able to transcribe genes important for red blood cell production, metabolic activity, angiogenesis,development, and many other functions.

=== Active Site===

The <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site/6'>FIH Active Site</scene> contains an iron (II) core. The iron core is coordinated by 2 histidine residues, an aspartate residue, an α-ketoglutarate molecule (α-KG), and one water molecule. The iron (II) is six coordinated, with α-KG chelating in a bidentate manner. The coordination of the active site ligands can be seen <scene name='User:John_Hangasky/Sandbox_1/Fih_active_site_ligands/7'>here</scene>. The axial coordination position is initially occupied by a water molecule. Upon binding of CTAD, this water molecule is released, opening a coordination site for oxygen to bind.

=== Enzyme Surface ===

In this depiction, the <scene name='User:John_Hangasky/Sandbox_1/Fih_surface/4'>solvent accessible surface</scene> of FIH is shown.

===3D structures of FIH===

[[Factor inhibiting HIF]]

==Additional Resources==
For additional information, see: [[Cancer]]

Vanessa Chaplin/sandbox1

2013-10-23T16:31:18Z

Vanessa Chaplin: New page: <Structure load='7DHR' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />