2id2

From Proteopedia

(Difference between revisions)

Current revision

GAPN T244S mutant X-ray structure at 2.5 A

Structural highlights

2id2 is a 4 chain structure with sequence from Streptococcus mutans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GAPN_STRMU

Evolutionary Conservation

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

Publication Abstract from PubMed

One of the most striking features of several X-ray structures of CoA-independent ALDHs (aldehyde dehydrogenases) in complex with NAD(P) is the conformational flexibility of the NMN moiety. However, the fact that the rate of the acylation step is high in GAPN (non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase) from Streptococcus mutans implies an optimal positioning of the nicotinamide ring relative to the hemithioacetal intermediate within the ternary GAPN complex to allow an efficient and stereospecific hydride transfer. Substitutions of serine for invariant Thr244 and alanine for Lys178 result in a drastic decrease of the efficiency of hydride transfer which becomes rate-limiting. The crystal structure of the binary complex T244S GAPN-NADP shows that the absence of the beta-methyl group leads to a well-defined conformation of the NMN part, including the nicotinamide ring, clearly different from that depicted to be suitable for an efficient hydride transfer in the wild-type. The approximately 0.6-unit increase in pK(app) of the catalytic Cys302 observed in the ternary complex for both mutated GAPNs is likely to be due to a slight difference in positioning of the nicotinamide ring relative to Cys302 with respect to the wild-type ternary complex. Taken together, the data support a critical role of the Thr244 beta-methyl group, held in position through a hydrogen-bond interaction between the Thr244 beta-hydroxy group and the epsilon-amino group of Lys178, in permitting the nicotinamide ring to adopt a conformation suitable for an efficient hydride transfer during the acylation step for all the members of the CoA-independent ALDH family.

Invariant Thr244 is essential for the efficient acylation step of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans.,Pailot A, D'Ambrosio K, Corbier C, Talfournier F, Branlant G Biochem J. 2006 Dec 15;400(3):521-30. PMID:16958622^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Pailot A, D'Ambrosio K, Corbier C, Talfournier F, Branlant G. Invariant Thr244 is essential for the efficient acylation step of the non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from Streptococcus mutans. Biochem J. 2006 Dec 15;400(3):521-30. PMID:16958622 doi:10.1042/BJ20060843

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2id2"

@@ Line 1: / Line 1: @@
 ==GAPN T244S mutant X-ray structure at 2.5 A==
-<StructureSection load='2id2' size='340' side='right' caption='[[2id2]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='2id2' size='340' side='right'caption='[[2id2]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2id2]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25175 Atcc 25175]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ID2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ID2 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2id2]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_mutans Streptococcus mutans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ID2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ID2 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">gapN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1309 ATCC 25175])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAP:NADP+NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NAP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glyceraldehyde-3-phosphate_dehydrogenase_(NADP(+)) Glyceraldehyde-3-phosphate dehydrogenase (NADP(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.9 1.2.1.9] </span></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=2id2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2id2 OCA], [https://pdbe.org/2id2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2id2 RCSB], [https://www.ebi.ac.uk/pdbsum/2id2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2id2 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2id2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2id2 OCA], [http://pdbe.org/2id2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2id2 RCSB], [http://www.ebi.ac.uk/pdbsum/2id2 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/GAPN_STRMU GAPN_STRMU]
 == 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/id/2id2_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/id/2id2_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2id2 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 29: / Line 31: @@
 ==See Also==
-*[[Aldehyde dehydrogenase|Aldehyde dehydrogenase]]
+*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
-*[[Glyceraldehyde-3-Phosphate Dehydrogenase|Glyceraldehyde-3-Phosphate Dehydrogenase]]
+*[[Amicyanin 3D structures|Amicyanin 3D structures]]
+*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 25175]]
+[[Category: Large Structures]]
-[[Category: Ambrosio, K D]]
+[[Category: Streptococcus mutans]]
-[[Category: Branlant, G]]
+[[Category: Branlant G]]
-[[Category: Corbier, C]]
+[[Category: Corbier C]]
-[[Category: Pailot, A]]
+[[Category: D'Ambrosio K]]
-[[Category: Talfournier, F]]
+[[Category: Pailot A]]
-[[Category: Acylation step]]
+[[Category: Talfournier F]]
-[[Category: Aldh]]
-[[Category: Conformation of nicotinamide]]
-[[Category: Hydride transfer]]
-[[Category: Oxidoreductase]]
-[[Category: T244]]

2id2

From Proteopedia

Current revision

GAPN T244S mutant X-ray structure at 2.5 A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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