Proteopedia - User contributions [en]

CBI Molecules

2012-12-12T20:50:13Z

Serap Pektas:

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 2012: CBI Molecules are due 12/12/12 and should be added at the TOP of the list from your lab. Label it as "in progress" until you are finished. 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 -- I may be able to request additions to the author list).

==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://openwetware.org/wiki/Chien Chien Lab]

: **'''[[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]

: ''' [[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/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

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

: ''' [[Molecular Playground/Transferrin]]''', Khaja Muneeruddin

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

Knapp lab

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

: '''[[Molecular Playground/FIH]]''', Cornelius Taabazuing, Breanne Holmes, John Hangasky

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

: '''[[Molecular Playground/Nickel Superoxide Dismutase]]''', Carolyn Carr
: '''[[Molecular Playground/CsoR and RcnR]]''', 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

Peyton Lab
: '''[[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

Schnarr Lab

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

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

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

: '''[[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

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==

'''Congratulations to the prize-winning CBI molecules noted above! The new 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 2012: Complete steps 1-3 by 10/10/12, in preparation for the CBI Molecule Workshop.

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

2. 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).

3. Get together with the other Chalk Talk students in your research group and decide which molecule you will improve or create. Develop ideas for the scenes you wish to show. You will work on these during the workshop with our help, and then finish them on your own.

You are encouraged to collaborate on this year's 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.

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.

4. 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.

==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

2012-12-12T20:45:51Z

Serap Pektas:

<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].

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

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

[[Hypoxia-inducible factor prolyl hydroxylase]]

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

Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme

2012-12-12T20:43:11Z

Serap Pektas:

<applet load='2g19' size='[350,338]' frame='true' align='right'
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].

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

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

[[Hypoxia-inducible factor prolyl hydroxylase]]

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

Molecular Playground/Prolyl Hydroxylase Domain (PHD) Enzyme

2012-12-12T20:25:08Z

Serap Pektas:

<applet load='2g19' size='[350,338]' frame='true' align='right'
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].

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 ===
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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. 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 ===
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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

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

[[Hypoxia-inducible factor prolyl hydroxylase]]

=== References ===
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<references/>

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Serap Pektas: uploaded a new version of "Image:Pymol.png"

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Serap Pektas: surface charge of p53 DNA binding domain

surface charge of p53 DNA binding domain

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Serap Pektas: p53 DNA biding domain binds to DNA

p53 DNA biding domain binds to DNA

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Serap Pektas: The cartoon respresentation of human p53 DNA binding domain.

The cartoon respresentation of human p53 DNA binding domain.

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Serap Pektas: Removing all content from page

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Serap Pektas: New page: <applet load='2H1L' size='300' frame='true' align='right' caption='p53 SV40' />

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