1dc6: Difference between revisions

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New page: left|200px<br /><applet load="1dc6" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dc6, resolution 2.0Å" /> '''STRUCTURAL ANALYSIS O...
 
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[[Image:1dc6.jpg|left|200px]]<br /><applet load="1dc6" size="450" color="white" frame="true" align="right" spinBox="true"
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'''STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES.'''<br />


==Overview==
==STRUCTURAL ANALYSIS OF GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE FROM ESCHERICHIA COLI: DIRECT EVIDENCE FOR SUBSTRATE BINDING AND COFACTOR-INDUCED CONFORMATIONAL CHANGES.==
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 load='1dc6' size='340' side='right'caption='[[1dc6]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dc6]] 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=1DC6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DC6 FirstGlance]. <br>
</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>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dc6 OCA], [https://pdbe.org/1dc6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dc6 RCSB], [https://www.ebi.ac.uk/pdbsum/1dc6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dc6 ProSAT]</span></td></tr>
</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/1dc6_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=1dc6 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1DC6 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NAD as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.12 1.2.1.12] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DC6 OCA].
*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
 
*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
==Reference==
__TOC__
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10978154 10978154]
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[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: NAD]]
[[Category: cofactor]]
[[Category: gapdh]]
[[Category: structure]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:09:38 2007''

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

Structural highlights

1dc6 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
Ligands:
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

1dc6, resolution 2.00Å

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