This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1gdh

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1gdh" size="450" color="white" frame="true" align="right" spinBox="true" caption="1gdh, resolution 2.4&Aring;" /> '''CRYSTAL STRUCTURE OF ...)
Current revision (07:24, 7 February 2024) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1gdh.gif|left|200px]]<br /><applet load="1gdh" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1gdh, resolution 2.4&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION==
-
D-Glycerate dehydrogenase (GDH) catalyzes the NADH-linked reduction of, hydroxypyruvate to D-glycerate. GDH is a member of a family of, NAD-dependent dehydrogenases that is characterized by a specificity for, the D-isomer of the hydroxyacid substrate. The crystal structure of the, apoenzyme form of GDH from Hyphomicrobium methylovorum has been determined, by the method of isomorphous replacement and refined at 2.4 A resolution, using a restrained least-squares method. The crystallographic R-factor is, 19.4% for all 24,553 measured reflections between 10.0 and 2.4 A, resolution. The GDH molecule is a symmetrical dimer composed of subunits, of molecular mass 38,000, and shares significant structural homology with, another NAD-dependent enzyme, formate dehydrogenase. The GDH subunit, consists of two structurally similar domains that are approximately, related to each other by 2-fold symmetry. The domains are separated by a, deep cleft that forms the putative NAD and substrate binding sites. One of, the domains has been identified as the NAD-binding domain based on its, close structural similarity to the NAD-binding domains of other, NAD-dependent dehydrogenases. The topology of the second domain is, different from that found in the various catalytic domains of other, dehydrogenases. A model of a ternary complex of GDH has been built in, which putative catalytic residues are identified based on sequence, homology between the D-isomer specific dehydrogenases. A structural, comparison between GDH and L-lactate dehydrogenase indicates a convergence, of active site residues and geometries for these two enzymes. The, reactions catalyzed are chemically equivalent but of opposing, stereospecificity. A hypothesis is presented to explain how the two, enzymes may exploit the same coenzyme stereochemistry and a similar, spatial arrangement of catalytic residues to carry out reactions that, proceed to opposite enantiomers.
+
<StructureSection load='1gdh' size='340' side='right'caption='[[1gdh]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1gdh]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Hyphomicrobium_methylovorum Hyphomicrobium methylovorum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GDH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GDH FirstGlance]. <br>
-
1GDH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Hyphomicrobium_methylovorum Hyphomicrobium methylovorum] with SO4 as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glycerate_dehydrogenase Glycerate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.29 1.1.1.29] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1GDH OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1gdh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gdh OCA], [https://pdbe.org/1gdh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gdh RCSB], [https://www.ebi.ac.uk/pdbsum/1gdh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gdh ProSAT]</span></td></tr>
-
Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 A resolution., Goldberg JD, Yoshida T, Brick P, J Mol Biol. 1994 Mar 4;236(4):1123-40. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8120891 8120891]
+
</table>
-
[[Category: Glycerate dehydrogenase]]
+
== Function ==
 +
[https://www.uniprot.org/uniprot/DHGY_HYPME DHGY_HYPME] Active on hydroxypyruvate and glyoxylate.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gd/1gdh_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1gdh ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
[[Category: Hyphomicrobium methylovorum]]
[[Category: Hyphomicrobium methylovorum]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Brick, P.]]
+
[[Category: Brick P]]
-
[[Category: Goldberg, J.D.]]
+
[[Category: Goldberg JD]]
-
[[Category: Yoshida, T.]]
+
[[Category: Yoshida T]]
-
[[Category: SO4]]
+
-
[[Category: oxidoreductase(choh (d)-nad(p)+ (a))]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 15:57:54 2007''
+

Current revision

CRYSTAL STRUCTURE OF A NAD-DEPENDENT D-GLYCERATE DEHYDROGENASE AT 2.4 ANGSTROMS RESOLUTION

PDB ID 1gdh

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1gdh"
Personal tools