Proteopedia - User contributions [en]

Sandbox 1

2009-01-18T12:54:17Z

Dan Bolser:

This is a sample <ref>Richardson DC, Richardson JS. The kinemage: a tool for scientific communication.
Protein Sci. 1992 1:3-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1304880 1304880]</ref> of the
standard references and one <ref>PMID:18673581</ref> with the PubmedID only new option <nowiki>"<ref>PMID:18673581</ref>"</nowiki>.

It's possible now to have additional references by adding them to the group '''xtra'''.
See this page source under ''Additional Literature and Resources''.

== References ==
<references/>

== Additional Literature and Resources ==
<ref group="xtra">PMID:15068885</ref>
<ref group="xtra">PMID:14749769</ref>
<ref group="xtra">PMID:1304880</ref>
<ref group="xtra">PMID:16270100</ref>
<ref group="xtra">PMID:14661029</ref>
<references group="xtra"/>

Sandbox 1

2009-01-18T12:53:22Z

Dan Bolser: testing 'group specificity' of references tag

This is a sample <ref>Richardson DC, Richardson JS. The kinemage: a tool for scientific communication.
Protein Sci. 1992 1:3-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1304880 1304880]</ref> of the
standard references and one <ref>PMID:18673581</ref> with the PubmedID only new option <nowiki><ref>PMID:18673581</ref> </nowiki>

It's possible now to have additional references by adding them to the group '''xtra'''.
See this page source under ''Additional Literature and Resources''.

== References ==
<references/>

== Additional Literature and Resources ==
<ref group="xtra">PMID:15068885</ref>
<ref group="xtra">PMID:14749769</ref>
<ref group="xtra">PMID:1304880</ref>
<ref group="xtra">PMID:16270100</ref>
<ref group="xtra">PMID:14661029</ref>
<references group="xtra"/>

User:Dan Bolser

2009-01-17T22:39:30Z

Dan Bolser: Added my first reference ;-)

{{User:DanBolser/1dan}}

Hello!

See my profile on [http://network.nature.com/profile/dan Nature Networks] or on [http://openwetware.org/wiki/User:Dan_Bolser Open Wet Ware].

In my spare time I work on [http://PDBWiki.org PDBWiki]<ref>PMID:18535227</ref>!

== References ==
<references />

User talk:Eran Hodis

2009-01-05T14:00:26Z

Dan Bolser: /* RE: */

==News from Greece==
Hi Eran,
actually I was on vacation after the summer school of Erice!
The last days I'm back in the lab and try to find the rythm of the experiments ;)
I shown to my boss the proteopedia and my page..he is excited! Actually I'm writing a paper and I may use the proteopedia for making the pictures. I would like to ask you how can I export the pictures to my pc.
We'll be in contact..you'll see the progress of my page!

best wishes
Maria
---------

Hi Eran,
Now back at home with access to my Mac. Much enjoyed meeting and talking with you. Carole and I enjoyed our round trip of Sicily, and we more or less walked our feet off in Pompei last Monday. Off to practice our golf swings now. I also talked to one of the head honchos of the Cambridge small molecule crystallographic database, and he was receptive to the idea of making a filterered subset of drugs and other biologically-active small molecules available to Proteopedia (read: ligands). If you are ever in the neighbourhood of Basel, look us up, and we can offer you a free place to sleep.
best regards
Trevor
---------

== Bad green link ==
Eran,
I have a green link which does not work, it should make a Ramachandran plot. When I attempt to edit it the SAT freezes and no other scenes can be loaded. In fact as I remember when I first made the scene the SAT froze. After the SAT freezes some of the links above and below this bad link no longer work. Is there a way that a developer can delete scenes?

Karl

---------
After I left the message for you, I decided to take a different approach and not use the link, but I would be interested in knowing what is wrong with the link if you can discover that. I named the link plot_tripep_disallowed.

Karl

== PDBsum site ==
Eran,
After exploring this site I have come to the conclusion that the entry page to this site changes from time to time. Is that correct? If so, I should give directions on the Ramachandran page how to generate the Ramachandran plot on PDBsum.

By the way that site is a wonderful resource. I am going to include it in the computer resource exercise that I have my Biochemistry I students do.

Karl

Eran,
I just realized that I was not thinking clearly this morning. I had forgotten that the url that I am using is coded for 1eve and Procheck, and therefore the site will open with the desired protein and information displayed.

Karl

== Proteopedia for teaching ==
Hi Eran

I'm in the middle of my labs using Proteopedia, and on balance I think it's a great improvement for this class - I run 6 streams of 60 students each in a 2nd year biochemistry class. Using sPDBv meant that they spent a lot of time struggling with the program, but proteopedia is letting them just think about the protein structure instead. So, overall positive. However, two things that have come up:

1) Secondary structure definitions - How does Jmol generate them? Are they user definable? Jmol is clearly using a different algorithm to sPDBv, so students are seeing inconsistency when they use both routes. (For the record, I agree with sPDBv's pick!)

2) More seriously, the display of backbone hydrogen bonds is wrong - not sure if this is something I'm doing wrong or a fault in Jmol. Backbone hydrogen bonds are being drawn between C-alphas rather than between carbonyl oxygens and peptide nitrogens. Check out the link at the very bottom of the page http://www.proteopedia.org/wiki/index.php/User:J._Shaun_Lott/BIOSCI_203 marked "What is wrong with this picture?" to see what I mean.

cheers!

Shaun

== What to do with my students contributions ==

Hi Eran,

I am trying user talk to communicate instead of my email, since my question may be relevant to other educators. I have several student contributions that I wish to keep and others that ought to be erased eventually. I want to keep the good ones, and one bad one for illustration of a range of student abilities. I am not sure if its best to transfer the material to my page; start another page with student contributions, or to link to the student's pages. I have the passwords the student sites, so I can access the scripts. What do you suggest is best?

Tom

== Surfaces ==

Hi Eran,

I tried but could not figure out if a surface of one protomer could be colored differently from a surface of another protomer using the surface representation.

Tom

== more on surfaces ==

Hi

Surfaces are slow to load--such is life--but my experience is the same as yours. Only one color is available for the surfaces. 
my best 
Tom 
PS. So, what is the Israeli greetings/salutation during Hannukah?

== Cheers Eran! ==

Thanks for the info. About the template text - it even appears here when I click the + tab in your talk page. I think it should be easy enough to limit the feature by namespace, as many WP extensions seem to be ns specific.

BTW, did you ever consider installing something like 'liquid threads' to make discussion more 'fully featured'? I played with it on a small wiki, and it worked OK, but when you install it you loose all old discussions. For a while I wanted to merge something like PHP BB with WP to create a forum 'channel' for each page, which should be simple enough to do... --[[User:Dan Bolser|Dan Bolser]] 10:58, 5 January 2009 (IST)

== RE: ==

Agreed about the template text. I'll email/message you when we have it updated. As to liquid threads, we've never considered anything like that, although its clear that the current MediaWiki system of messages is less than intuitive to say the least. We'd be hesitant to make large changes whose stability is not guaranteed, but if you think this is something we should look into, please link me to the appropriate places where I can read more about it. Eran Hodis 13:59, 5 January 2009 (IST)

: With respect to 'is [this] something we should look into', I'm not really sure. It depends on how much you want Proteopedia to function as a 'community discussion forum' in addition to being a 'community education portal'. Actually, something like 'technical community discussion' was the emphasis of PDBWiki, which is why we think that it stands distinct from Proteopedia (with its emphasis on education). So basically I think its up to you to look at what is possible and assess the potential benefit, which may be marginal. Liquid threads is at http://www.mediawiki.org/wiki/Extension:LiquidThreads However, as I said, I'd be more interested in seeing a mini 'PHP BB' appearing within each talk tab http://www.phpbb.com/ I don't know why there are no efforts to implement this (that I can find). Oh... I spoke to soon ;-D http://www.mediawikiusers.com/wiki/index.php/Projects:MediaWiki/phpBB_Integration but that seems a bit thin on details TBH... Anyway, I only mentioned this because you seem to have a good capacity to work on such features, and I think that such a feature would be generally useful to the wider wiki world. All the best --[[User:Dan Bolser|Dan Bolser]] 15:24, 5 January 2009 (IST)

:: After poking around I found this, http://www.mediawiki.org/wiki/Extension:AWC's_Forum which looks very promising. --[[User:Dan Bolser|Dan Bolser]] 16:00, 5 January 2009 (IST)

User talk:Eran Hodis

2009-01-05T13:24:45Z

Dan Bolser: RE:

User talk:Eran Hodis

2009-01-05T08:58:36Z

Dan Bolser: Cheers Eran!

Talk:Believe It or Not!

2009-01-05T08:55:12Z

Dan Bolser:

== Page? ==
How is this page maintained / Who maintains this page? My point is, how up to date are the statistics? Is there an automatic procedure for updating the statistics? Cheers, --[[User:Dan Bolser|Dan Bolser]] 13:39, 4 January 2009 (IST)

: Hi Dan, The page is updated automatically via a script that [[User:Jaime Prilusky| Jaime Prilusky]] developed. It uses information from the OCA database and you'll find on the page the date of the last update (in this case it says Wed Dec 31st). The update process is weekly. Best, [[User:Eran Hodis|Eran Hodis]] 14:46, 4 January 2009 (IST)

:: Thanks for the info Eran!

Talk:Believe It or Not!

2009-01-04T11:39:19Z

Dan Bolser: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click "Show Preview" at the bottom of this page to see how...

==This is a placeholder==
This is a placeholder text to help you get started in
placing a Jmol applet on your page. At any time, click
"Show Preview" at the bottom of this page to see how it goes.

Replace the PDB id after the STRUCTURE_ and after PDB= to load
and display another structure.

{{STRUCTURE_3cin | PDB=3cin | SCENE= }}

== Page? ==
How is this page maintained / Who maintains this page? My point is, how up to date are the statistics? Is there an automatic procedure for updating the statistics? Cheers, --[[User:Dan Bolser|Dan Bolser]] 13:39, 4 January 2009 (IST)

Talk:Resolution

2009-01-04T10:08:30Z

Dan Bolser: New page: Some rough notes added below for potential incorperation into the article (delete below when added ;-) :--~~~~ == Post to PDB-L == Some time back I remember reading a posting to this li...

Some rough notes added below for potential incorperation into the article (delete below when added ;-)
:--[[User:Dan Bolser|Dan Bolser]] 12:08, 4 January 2009 (IST)

== Post to PDB-L ==

Some time back I remember reading a posting to this list where some very general rules-of-thumb were given for interpreting the value of the resolution of an X-ray structure.

The rules were something like (very approximate version!)

* >4 Angstrom = Unlikely to even get backbone right (anything goes).
* >3 Angstrom = Backbone possible but side chain orientation is probably wrong.
* >2 Angstrom = Sidechain orientation is broadly correct, but 'some other problems' exist.
* >1 Angstrom = 'Some other problems' are probably gone.
* >0.5 Angstrom = Hydrogen atoms are 'visible'.

Where (if I remember correctly) the 'some other problems' were issues of sterio-chemistry, orientation of specific groups, etc.

Please note, if I remembered incorrectly the above 'rules' may be totally wrong!

== Reply ==

I would refer you to a very nice talk Greg Warren (at Openeye) gave at the ACS meeting.

In this presentation he gave multiple examples of problematic situations many of us have seen. The bottom line is that even with apparently high resolution (<2A) many serious problems can remain due to poorly fit density, missing local density, multiple solutions to the fit, and especially ligand issues.

At least as important as resolution is Rfree, which gives you a measure of how well the model structure fits the electron density generated from structure factors (the actual experimental data).

In a general sense the table you cite is not too bad I suppose, but the problem is that there is not a general answer. A very good structure might be bad where it matters to you, and a low resolution structure, say 3A, might not be as bad as you think.

Dominic Ryan

== Reply ==

I would also add that "quality" is not something that
depends solely on resolution, but also very heavily on
the environment of the residue. At 2.8A to 3A
resolution, for example, it's still possible to
determine the orientation of buried residues, but
things may be really ugly on the surface. So, if what
you want is have a measure about "what to trust" in a
x-ray structure, it's a good idea to check the
real-space correlation by residue (a coeficient that
tells how well the modeled structure fits in the
electron density), or visually check what's going on
using the electron density server at
http://eds.bmc.uu.se/eds/

Talk:Hydrogen in macromolecular models

2008-11-24T09:38:55Z

Dan Bolser: Added back the Content Attribution text.

==Content Attribution==

This page is adapted from documentation written earlier by [[User:Eric Martz]], with permission, for several locations in [[Protein Explorer]]: [http://proteinexplorer.org/iv_water.htm Water], [http://proteinexplorer.org/help_hyd.htm Hydrogens in PDB files], and ''Hydrogen'' in the [http://proteinexplorer.org/igloss.htm Help/Index/Glossary].

Thanks to John Badger for key contributions.

:I moved the above attribution text from the article to the discussion page. Attribution is handled differently in the Wiki system than in the text on which this article was based. --[[User:Dan Bolser|Dan Bolser]] 11:38, 24 November 2008 (IST)

Hydrogen in macromolecular models

2008-11-24T09:37:06Z

Dan Bolser: Added an page summary (which is good style), removed 'Content Attribution' (this is wiki), and 'wikified' the table.

Approximately 50% of the atoms in a protein are hydrogen. However, hydrogen atoms are absent from most molecular models. Most crystals do not have sufficient resolution (1.0 Ångstroms or less) to determine the positions of hydrogen atoms. It is easy to add hydrogens to macromolecular models, but the results are only as good as the molecular models themselves.

==Absence of Hydrogen Atoms in Most Macromolecular Models==

Hydrogen atoms are absent from most molecular models in Proteopedia, which come mostly from the [[Protein Data Bank]]. This is because most macromolecular crystals do not have sufficient [[resolution]] to determine the positions of hydrogen atoms. However it is easy to [[#Adding Hydrogens|add hydrogen atoms]], and in fact it is a good idea, because it [[#Model Validation??|helps to correct and validate]] the molecular model.

Although their positions are not well defined empirically in the electron density maps from typical macromolecular crystals, sometimes [[#Adding Hydrogens|hydrogens are added]] to X-ray crystallographic models before they are deposited in the Protein Data Bank. This is the choice of the authors of the [[PDB file]]. Hydrogens are usually present in PDB files resulting from [[NMR]] analysis, and usually present in [[theoretical models]].

==Approximately 50% of Protein Atoms, and approximately 35% of Nucleic Acid Atoms, are Hydrogen==

In proteins, the average number of hydrogens per non-hydrogen atom, weighted to take into account the frequencies of amino acids, is 1.01. Thus, hydrogens are ~50% of all atoms in protein. Nucleic acids have fewer, ~35%.

To '''determine the percentage of atoms that are hydrogen''' in a model in Proteopedia, click on the word ''Jmol'' in the lower right corner of the rotatable molecular scene, and then on ''Console''. In the lower box of the Console window that opens, enter "select hydrogen" and note the atom count in the report in the upper box. Then do the same for "select not hydrogen".

To '''visualize hydrogen atoms''', use the ''FirstGlance'' link in the ''Resources'' section beneath the molecular scene. Once the model is displayed in [[FirstGlance in Jmol]], click on ''Vines''. Change the background to black with the background toggle button. Now click on ''Vines''. In the help panel for ''Vines'', check ''More detail''. Hydrogen atoms are white. To hide and then show them, check ''Hide hydrogens'', then uncheck it.

<blockquote>
The value 1.01, for the average number of protein hydrogens per non-hydrogen protein atom, was calculated from the values for each amino acid, weighted by average frequencies of amino acids. The frequencies employed are based on 1,021 unrelated proteins of known sequence, tabulated on page 5 in Creighton (1993)<ref>"Proteins, Structures and Molecular Properties", Thomas E. Creighton, 2nd ed., 1993, W. H. Freeman and Co.</ref>.
</blockquote>

==Hydrogens Present in Macromolecular Models==

===Empirically-Positioned Hydrogens in High-Resolution Crystallographic Models===

High resolution protein crystallography (1.2 Ångstroms or less) can assign some hydrogen positions empirically from the electron density map, and very high resolution crystals (1.0 Ångstroms or less) can assign the positions of most hydrogens.

* '''Example:''' The X-ray model of a tyrosine kinase SH2 domain [[1lkk]] at 1.0 Angstrom resolution contains 901 hydrogens and 920 non-hydrogen protein atoms (ratio 0.98, 49%), so approximately all of the hydrogens actually present are assigned positions.

===Theoretically-Positioned Hydrogens in Average-Resolution Crystallographic Models===

As explained above, most macromolecular crystals do not provide high enough resolution to detect hydrogen positions empirically. The median [[resolution]] of models in the [[Protein Data Bank]] is 2.0 Å.

*'''Example: No hydrogens''': The X-ray model in PDB file [[1hho]] for oxyhemoglobin (2.1 A resolution) contains no hydrogens.

*'''Example: Some hydrogens from theory''': The X-ray file [[1lfa]] (1.8 A resolution; an integrin adhesion protein domain) contains 312 waters each with 2 hydrogens (so 624 water hydrogens), plus 639 protein hydrogens for 2,939 non-hydrogen protein atoms, which account for only 22% (639/2,939) of the hydrogens actually present in this protein. The protein hydrogens consist of one hydrogen on each backbone nitrogen (three hydrogens/amino terminal nitrogen), and hydrogens on sidechain oxygens or nitrogens in Ser, Thr, Tyr, Lys, Arg, His, Asn, and Gln. None of the hydrogens covalently bonded to carbons are present. The hydrogens which are present are required for the molecular dynamics stages of refinement of the X-ray model in the popular crystallographic refinement program X-PLOR; some authors strip them out before submitting a [[PDB file]] and others leave them in. The [[Protein Data Bank]] accepts X-ray models either way, according to the preference of the depositor.

*'''Example: All hydrogens from theory''':

===Hydrogens in NMR Models===

[[NMR]] methods also determine some hydrogen positions. Typically all hydrogens are modeled in before the molecule is folded to fit the NMR interatomic distance restraints; hence, all hydrogens are usually present in NMR models submitted to the PDB.

*'''Example:''' The calmodulin ensemble of 25 [[NMR]] models [[1cfc]] contains 1096 protein hydrogens and 1166 non-hydrogen protein atoms per model (ratio 0.94, 48.5%), thereby assigning positions for approximately all of the hydrogens actually present.

==Adding Hydrogens From Theory==

It is easy to add hydrogens to macromolecular models ([[PDB files]]) using the highly-reliable free servers listed below. Beware that the results are only as good as the molecular models themselves. Uncertainties in the positions of non-hydrogen atoms will, of course, produce inaccurate positions for hydrogen atoms. In fact, the quality of the molecular model can be judged in part from how well the hydrogens fit into the spaces between the non-hydrogen atoms. This degree of fit is quantitated in the ''overall clash score'' reported by the first method below, ''Molprobity''.

* Use the Richardson Lab's easy and very powerful [http://molprobity.biochem.duke.edu/ MolProbity: All-Atom Contact Analysis] server. Hydrogens are added to both protein and nucleic acids (but not to water), and you can save the resulting [[PDB file]]. This server has the advantage that you also get a powerful analysis of the quality of the model, including which Gln/Asn/His residues should have their sidechains flipped, an overall clash score, etc. You can save a model with the recommended sidechains flipped. Also you can visualize clashes anywhere in the model, including with the sidechains flipped or not flipped.

* Use the Vriend Lab's [http://swift.cmbi.ru.nl/servers/html/index.html WHATIF WWW Interface]. Hydrogens are added to both protein and nucleic acids '''and also to water'''.
**Under Classes (at left) click "Hydrogen (bonds)".
**Select "Add protons to the structure".
**Enter your PDB ID or upload a coordinate file.
**After the results appear, click on the pdb link to receive the coordinate file containing added hydrogens.

[[PDB files]] that you save from either of these methods, can, for example, be uploaded for visualization in [[FirstGlance in Jmol]].

[[1d66]] is an early (1992) modest resolution (2.7 Å) crystallographic model containing protein, DNA and 51 water oxygens. MolProbity reports its clashscore as 11.7, 65th percentile. The model deposited in the [[PDB]] contains no hydrogen atoms. The results from the above two servers:

{| class="wikitable" style="text-align:right"
|+ Comparing MolProbity and WHATIF on 1d66
! Server !! Protein Hydrogens !! Nucleic Hydrogens !! Water Hydrogens !! Total Hydrogens
|-
| MolProbity || 982 || 427 || 0 || 1,409
|-
| WHATIF || 1,000 || 423 || 102 || 1,525
|}
'''1d66:''' WHATIF protonates the sulfurs in 12 cysteines that are coordinating 4 cadmium ions, and the 2 N terminal nitrogens (6 H atoms), while MolProbity does not. MolProbity protonates the terminal hydroxyls on the 2 DNA chains, while WHATIF does not. All hydrogens added by MolProbity appeared to be in reasonable geometries, while some of those added by WHATIF were not.

==See Also==
*[[Quality assessment for molecular models]]

==Notes & References==
<references />

Talk:Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System

2008-10-20T08:41:04Z

Dan Bolser: New page: I think I made a mistake linking several instances of the word 'Phosphoenolpyruvate' to this page (you can find them by clicking 'what links here' ... Should I undo these links? I think I ...

I think I made a mistake linking several instances of the word 'Phosphoenolpyruvate' to this page (you can find them by clicking 'what links here' ... Should I undo these links? I think I got confused thinking that Phosphoenolpyruvate was the name of the enzyme described by this page. I now think that this is a mistake. --[[User:Dan Bolser|Dan Bolser]] 10:41, 20 October 2008 (IST)

Category:Phosphoenolpyruvate

2008-10-20T08:39:21Z

Dan Bolser:

List of pages with the keyword [[Phosphoenolpyruvate]]

Phosphoenolpyruvate

2008-10-20T08:33:02Z

Dan Bolser: basic

#REDIRECT [[Enzyme I of the Phosphoenolpyruvate:Sugar Phosphotransferase System]]

User:Dan Bolser

2008-10-20T08:28:24Z

Dan Bolser: :-D

Pyruvate phosphate dikinase

2008-10-20T08:24:32Z

Dan Bolser: /* Pyruvate Phosphate Dikinase - a Molecular Machine */ fixed a typo

==Pyruvate Phosphate Dikinase - a Molecular Machine==

<div style="float:right;padding:10px;">
<swf width="390" height="390">https://carb.umbi.umd.edu/system/files/ppdk_release.swf</swf> 
You may also [https://carb.umbi.umd.edu/files/ppdk_release.mpg download] the full High Resolution video.
</div>
'''Pyruvate phosphate dikinase''' (PPDK) is an enzyme that catalyzes the inter-conversion of [[adenosine triphosphate]] (ATP), [[phosphate]] (Pi), and [[pyruvate]] with [[adenine monophosphate]] (AMP), [[pyrophosphate]] (PPi), and [[phosphoenolpyruvate]] (PEP) in the presence of Magnesium and potassium ions (Mg2+ and K+/Na+). The three-step reversible reaction proceeds via phosphoenzyme and pyrophosphoenzyme intermediates with a histidine residue serving as the phosphocarrier:

#PPDK-His + PEP ⇄ PPDK-His~PO3 + pyruvate
#PPDK-His~PO3 + P2O7 ⇄ PPDK-His~P2O7 + PO3
#PPDK-His~P2O7 + AMP ⇄ PPDK-His + ATP

The enzyme has been found in bacteria, in C4 and Crassulacean acid metabolism plants, and in parasites, but not in higher animal forms. In bacteria and parasites, PPDK functions in the direction of ATP synthesis (reminiscent of pyruvate kinase). In plants and in photosynthetic bacteria, PPDK functions in PEP formation, potentiating the rate of CO2 fixation that takes place during photosynthesis. PPDK exhibits sequence homology to pyruvate phosphate synthase, and to another enzyme that utilizes phosphotransfer from PEP to a histidine residues, Enzyme I of the PEP:sugar phosphotransferase system (PTS).

PPDK assembles into homodimers of ~95 kD subunit molecular mass. The monomer is comprised of three domains and contains two distinct reaction centers located ~45 Å apart; the PEP/pyruvate partial reaction (step 1) takes place at the C-terminal domain (adopting an α/β barrel fold) and the nucleotide and inorganic phosphate partial reactions (steps 2 and 3) take place at the N-terminal domain (adopting the ATP grasp fold with two sub domains). A central domain, tethered to the N- and C-terminal domains by two closely-associated linkers, contains a phosphorylatable histidine residue (His455). To shuttle the phosphoryl group between the two reaction centers, the His-domain undergoes domain motion of ~110° swivel around the two linkers. In addition, upon detachment from the His-domain, the two nucleotide-binding sub domains undergo a ~40° hinge motion that opens the active site cleft.
'''The His-domain in the two conformational states of PPDK. His455 is shown in blue spheres:'''[[Image:two_cond.jpg|left|600px]] 

'''''The movie''' depicts the catalytic reaction involving three in-line phosphotransfers and the accompanied protein conformational transitions. This is a model based on crystal structures of PPDK from '''Clostridium symbiosum''' in the two extreme conformational states shown to the left and of complexes bound to substrate analogs, phosphonopyruvate and 5'-adenylyl-β,γ-imidodiphosphate (AMPPNP). The nucleotide binding subdomains are colored green and blue. The PEP binding domain is colored cyan. The His-domain is colored yellow, and the linker segments that connect the His-domain to the partner domains are colored red. Ligands and the catalytic histidine are depicted in stick models with the atomic color scheme: Carbon – gray, Nitrogen – blue, Oxygen – red, Phosphorous – green, Magnesium – magenta. Note that the reaction pregresses in the movie in the reverse direction; steps 3 and 2 occur first followed by step 1. The movie was created by Kap Lim and osnat Herzberg'' 
 

== Key References ==

#Herzberg, O., Chen, C. C. H., Kapadia, G., McGuire, M., Carroll, L. J., Noh, S. J., Dunaway-Mariano, D. (1996) Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites, Proc Natl Acad Sci 93, 2652-2657.
#Herzberg, O., Chen, C. C. H., Liu, S., Tempczyk, A., Howard, A., Wei, M., Ye, D., Dunaway-Mariano, D. (2002) Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis, Biochemistry 41, 780-787.
#Lim, K., Read, R. J., Chen, C. C., Tempczyk, A., Wei, M., Ye, D., Wu, C., Dunaway-Mariano, D., and Herzberg, O. (2007) Swiveling domain mechanism in pyruvate phosphate dikinase, Biochemistry 46, 14845-14853.

==Selected 3D Structures of PPDK ==
* [[1dik]] This is the original determined structure for '''''C. symbiosum''''' PPDK.
* [[1kbl]] This is the highest resolution X-ray structure of PPDK determined till now.
* [[2r82]] PPDK triple mutant R219E/E271R/S262D that adapts a second conformational state
* [[1kc7]] PPDK bound with Mg-phosphonopyruvate inhibitor that bind in the PEP binding domain.
* [[2dik]] R337A PPDK - nucleotide binding site mutation.
* [[1jde]] K22A PPDK - nucleotide binding site mutation.
* [[1jde]] T453A PPDK - His-domain mutation.

Pyruvate phosphate dikinase

2008-10-20T08:22:44Z

Dan Bolser: wikified the ligand names (trying to understand the reaction)

==Pyruvate Phosphate Dikinase - a Molecular Machine==

<div style="float:right;padding:10px;">
<swf width="390" height="390">https://carb.umbi.umd.edu/system/files/ppdk_release.swf</swf> 
You may also [https://carb.umbi.umd.edu/files/ppdk_release.mpg download] the full High Resolution video.
</div>
'''Pyruvate phosphate dikinase''' (PPDK) is an enzyme that catalyzes the inter-conversion of [[adenosine triphosphate]] (ATP), [[phosphate]] (Pi), and [[pyruvate]] with [[adenine monophosphate]] (AMP), [[pyrophosphate]] (PPi), and [[phosphoenolpyruvate]] (PEP) in the presence of Magnesium and potassium ions (Mg2+ and K+/Na+). The three-step reversible reaction proceeds via phosphoenzyme and pyrophosphoenzyme intermediates with a histidine residue serving as the phosphocarrier:

#PPDK-His + PEP ⇄ PPDK-His~PO3 + pyruvate
#PPDK-His~PO3 + P2O7 ⇄ PPDK-His~P2O7 + PO3
#PPDK-His~P2O7 + AMP ⇄ PPDK-His + ATP

The enzyme has been found in bacteria, in C4 and Crassulacean acid metabolism plants, and in parasites, but not in higher animal forms. In bacteria and parasites, PPDK functions in the direction of ATP synthesis (reminiscent of pyruvate kinase). In plants and in photosynthetic bacteria, PPDK functions in PEP formation, potentiating the rate of CO2 fixation that takes place during photosynthesis.PPDK exhibits sequence homology to pyruvate phosphate synthase, and to another enzyme that utilizes phosphotransfer from PEP to a histidine residues, Enzyme I of the PEP:sugar phosphotransferase system (PTS).

PPDK assembles into homodimers of ~95 kD subunit molecular mass. The monomer is comprised of three domains and contains two distinct reaction centers located ~45 Å apart; the PEP/pyruvate partial reaction (step 1) takes place at the C-terminal domain (adopting an α/β barrel fold) and the nucleotide and inorganic phosphate partial reactions (steps 2 and 3) take place at the N-terminal domain (adopting the ATP grasp fold with two sub domains). A central domain, tethered to the N- and C-terminal domains by two closely-associated linkers, contains a phosphorylatable histidine residue (His455). To shuttle the phosphoryl group between the two reaction centers, the His-domain undergoes domain motion of ~110° swivel around the two linkers. In addition, upon detachment from the His-domain, the two nucleotide-binding sub domains undergo a ~40° hinge motion that opens the active site cleft.
'''The His-domain in the two conformational states of PPDK. His455 is shown in blue spheres:'''[[Image:two_cond.jpg|left|600px]] 

'''''The movie''' depicts the catalytic reaction involving three in-line phosphotransfers and the accompanied protein conformational transitions. This is a model based on crystal structures of PPDK from '''Clostridium symbiosum''' in the two extreme conformational states shown to the left and of complexes bound to substrate analogs, phosphonopyruvate and 5'-adenylyl-β,γ-imidodiphosphate (AMPPNP). The nucleotide binding subdomains are colored green and blue. The PEP binding domain is colored cyan. The His-domain is colored yellow, and the linker segments that connect the His-domain to the partner domains are colored red. Ligands and the catalytic histidine are depicted in stick models with the atomic color scheme: Carbon – gray, Nitrogen – blue, Oxygen – red, Phosphorous – green, Magnesium – magenta. Note that the reaction pregresses in the movie in the reverse direction; steps 3 and 2 occur first followed by step 1. The movie was created by Kap Lim and osnat Herzberg'' 
 

== Key References ==

#Herzberg, O., Chen, C. C. H., Kapadia, G., McGuire, M., Carroll, L. J., Noh, S. J., Dunaway-Mariano, D. (1996) Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites, Proc Natl Acad Sci 93, 2652-2657.
#Herzberg, O., Chen, C. C. H., Liu, S., Tempczyk, A., Howard, A., Wei, M., Ye, D., Dunaway-Mariano, D. (2002) Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis, Biochemistry 41, 780-787.
#Lim, K., Read, R. J., Chen, C. C., Tempczyk, A., Wei, M., Ye, D., Wu, C., Dunaway-Mariano, D., and Herzberg, O. (2007) Swiveling domain mechanism in pyruvate phosphate dikinase, Biochemistry 46, 14845-14853.

==Selected 3D Structures of PPDK ==
* [[1dik]] This is the original determined structure for '''''C. symbiosum''''' PPDK.
* [[1kbl]] This is the highest resolution X-ray structure of PPDK determined till now.
* [[2r82]] PPDK triple mutant R219E/E271R/S262D that adapts a second conformational state
* [[1kc7]] PPDK bound with Mg-phosphonopyruvate inhibitor that bind in the PEP binding domain.
* [[2dik]] R337A PPDK - nucleotide binding site mutation.
* [[1jde]] K22A PPDK - nucleotide binding site mutation.
* [[1jde]] T453A PPDK - His-domain mutation.

User:Dan Bolser

2008-09-05T15:45:42Z

Dan Bolser:

{{User:DanBolser/1dan}}

Hello!

See my profile on [http://network.nature.com/profile/dan Nature Networks] or on [http://openwetware.org/wiki/User:Dan_Bolser Open Wet Ware].

User:Dan Bolser/1dan

2008-04-09T15:26:35Z

Dan Bolser: 1dan!

User:Dan Bolser/1dan

2008-04-09T14:59:12Z

Dan Bolser: New page: {{Structure |PDB= 1dan |SIZE=350|CAPTION= <scene name='initialview01'>1dan</scene>, resolution 2.00Å |SITE= |LIGAND= <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene ...

{{Structure
|PDB= 1dan |SIZE=350|CAPTION= <scene name='initialview01'>1dan</scene>, resolution 2.00Å
|SITE=
|LIGAND= <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=CH2:METHYLENE+GROUP'>CH2</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DPN:D-PHENYLALANINE'>DPN</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>
|ACTIVITY= [http://en.wikipedia.org/wiki/Coagulation_factor_VIIa Coagulation factor VIIa], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.21 3.4.21.21] 
|GENE=
|DOMAIN=
|RELATEDENTRY=
|RESOURCES=[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dan FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dan OCA], [http://www.ebi.ac.uk/pdbsum/1dan PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dan RCSB]
}}

User:Dan Bolser

2008-04-09T14:58:38Z

Dan Bolser:

{{User:DanBolser/1dan}}

Hello!

http://openwetware.org/wiki/User:Dan_Bolser