1dc5: Difference between revisions

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==STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES==
The line below this paragraph, containing "STRUCTURE_1dc5", creates the "Structure Box" on the page.
<StructureSection load='1dc5' size='340' side='right'caption='[[1dc5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1dc5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC5 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</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&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc5 OCA], [https://pdbe.org/1dc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc5 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc5 ProSAT]</span></td></tr>
{{STRUCTURE_1dc5| PDB=1dc5 |  SCENE= }}
</table>
== Function ==
[https://www.uniprot.org/uniprot/G3P1_ECOLI G3P1_ECOLI]
== 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/dc/1dc5_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=1dc5 ConSurf].
<div style="clear:both"></div>


'''STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES'''
==See Also==
 
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
 
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
==Overview==
__TOC__
The crystal structures of gyceraldehyde 3-phosphate dehydrogenase (GAPDH) from Escherichia coli have been determined in three different enzymatic states, NAD(+)-free, NAD(+)-bound, and hemiacetal intermediate. The NAD(+)-free structure reported here has been determined from monoclinic and tetragonal crystal forms. The conformational changes in GAPDH induced by cofactor binding are limited to the residues that bind the adenine moiety of NAD(+). Glyceraldehyde 3-phosphate (GAP), the substrate of GAPDH, binds to the enzyme with its C3 phosphate in a hydrophilic pocket, called the "new P(i)" site, which is different from the originally proposed binding site for inorganic phosphate. This observed location of the C3 phosphate is consistent with the flip-flop model proposed for the enzyme mechanism [Skarzynski, T., Moody, P. C., and Wonacott, A. J. (1987) J. Mol. Biol. 193, 171-187]. Via incorporation of the new P(i) site in this model, it is now proposed that the C3 phosphate of GAP initially binds at the new P(i) site and then flips to the P(s) site before hydride transfer. A superposition of NAD(+)-bound and hemiacetal intermediate structures reveals an interaction between the hydroxyl oxygen at the hemiacetal C1 of GAP and the nicotinamide ring. This finding suggests that the cofactor NAD(+) may stabilize the transition state oxyanion of the hemiacetal intermediate in support of the flip-flop model for GAP binding.
</StructureSection>
 
==About this Structure==
1DC5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DC5 OCA].
 
==Reference==
Structural analysis of glyceraldehyde 3-phosphate dehydrogenase from Escherichia coli: direct evidence of substrate binding and cofactor-induced conformational changes., Yun M, Park CG, Kim JY, Park HW, Biochemistry. 2000 Sep 5;39(35):10702-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10978154 10978154]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Kim, J Y.]]
[[Category: Kim J-Y]]
[[Category: Park, C G.]]
[[Category: Park C-G]]
[[Category: Park, H W.]]
[[Category: Park H-W]]
[[Category: Yun, M.]]
[[Category: Yun M]]
[[Category: Gapdh]]
[[Category: Structure]]
[[Category: Substrate]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 13:40:44 2008''

Latest revision as of 09:51, 7 February 2024

STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGESSTRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES

Structural highlights

1dc5 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G3P1_ECOLI

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1dc5, resolution 2.00Å

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