1rm5

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of mutant S188A of photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform, complexed with NADP

Structural highlights

1rm5 is a 3 chain structure with sequence from Spinacia oleracea. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

G3PA_SPIOL

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

Chloroplast glyceraldehyde-3-phosphate dehydrogenase (GAPDH) of higher plants uses both NADP(H) and NAD(H) as coenzyme and consists of one (GapA) or two types of subunits (GapA, GapB). AB-GAPDH is regulated in vivo through the action of thioredoxin and metabolites, showing higher kinetic preference for NADPH in the light than in darkness due to a specific effect on kcat(NADPH). Previous crystallographic studies on spinach chloroplast A4-GAPDH complexed with NADP or NAD showed that residues Thr33 and Ser188 are involved in NADP over NAD selectivity by interacting with the 2'-phosphate group of NADP. This suggested a possible involvement of these residues in the regulatory mechanism. Mutants of recombinant spinach GapA (A4-GAPDH) with Thr33 or Ser188 replaced by Ala (T33A, S188A and double mutant T33A/S188A) were produced, expressed in Escherichia coli, and compared to wild-type recombinant A4-GAPDH, in terms of crystal structures and kinetic properties. Affinity for NADPH was decreased significantly in all mutants, and kcat(NADPH) was lowered in mutants carrying the substitution of Ser188. NADH-dependent activity was unaffected. The decrease of kcat/Km of the NADPH-dependent reaction in Ser188 mutants resembles the behaviour of AB-GAPDH inhibited by oxidized thioredoxin, as confirmed by steady-state kinetic analysis of native enzyme. A significant expansion of size of the A4-tetramer was observed in the S188A mutant compared to wild-type A4. We conclude that in the absence of interactions between Ser188 and the 2'-phosphate group of NADP, the enzyme structure relaxes to a less compact conformation, which negatively affects the complex catalytic cycle of GADPH. A model based on this concept might be developed to explain the in vivo light-regulation of the GAPDH.

Coenzyme site-directed mutants of photosynthetic A4-GAPDH show selectively reduced NADPH-dependent catalysis, similar to regulatory AB-GAPDH inhibited by oxidized thioredoxin.,Sparla F, Fermani S, Falini G, Zaffagnini M, Ripamonti A, Sabatino P, Pupillo P, Trost P J Mol Biol. 2004 Jul 23;340(5):1025-37. PMID:15236965^[1]

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

References

↑ Sparla F, Fermani S, Falini G, Zaffagnini M, Ripamonti A, Sabatino P, Pupillo P, Trost P. Coenzyme site-directed mutants of photosynthetic A4-GAPDH show selectively reduced NADPH-dependent catalysis, similar to regulatory AB-GAPDH inhibited by oxidized thioredoxin. J Mol Biol. 2004 Jul 23;340(5):1025-37. PMID:15236965 doi:10.1016/j.jmb.2004.06.005

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/1rm5"

@@ Line 1: / Line 1: @@
 ==Crystal structure of mutant S188A of photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform, complexed with NADP==
-<StructureSection load='1rm5' size='340' side='right' caption='[[1rm5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='1rm5' size='340' side='right'caption='[[1rm5]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1rm5]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Spiol Spiol]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RM5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RM5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1rm5]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RM5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RM5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jn0|1jn0]], [[1nbo|1nbo]], [[1rm3|1rm3]], [[1rm4|1rm4]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GapA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3562 SPIOL])</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=1rm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rm5 OCA], [https://pdbe.org/1rm5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rm5 RCSB], [https://www.ebi.ac.uk/pdbsum/1rm5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rm5 ProSAT]</span></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(+))_(phosphorylating) Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)) (phosphorylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.1.13 1.2.1.13] </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=1rm5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rm5 OCA], [http://pdbe.org/1rm5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rm5 RCSB], [http://www.ebi.ac.uk/pdbsum/1rm5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rm5 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/G3PA_SPIOL G3PA_SPIOL]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 15: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rm/1rm5_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 29: / Line 29: @@
 </div>
 <div class="pdbe-citations 1rm5" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Aldehyde dehydrogenase 3D structures|Aldehyde dehydrogenase 3D structures]]
+*[[Glyceraldehyde-3-phosphate dehydrogenase 3D structures|Glyceraldehyde-3-phosphate dehydrogenase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Spiol]]
+[[Category: Large Structures]]
-[[Category: Falini, G]]
+[[Category: Spinacia oleracea]]
-[[Category: Fermani, S]]
+[[Category: Falini G]]
-[[Category: Pupillo, P]]
+[[Category: Fermani S]]
-[[Category: Ripamonti, A]]
+[[Category: Pupillo P]]
-[[Category: Sabatino, P]]
+[[Category: Ripamonti A]]
-[[Category: Sparla, F]]
+[[Category: Sabatino P]]
-[[Category: Trost, P]]
+[[Category: Sparla F]]
-[[Category: Gapdh-nadp complex]]
+[[Category: Trost P]]
-[[Category: Oxidoreductase]]
-[[Category: Rossmann fold]]

1rm5

From Proteopedia

Current revision

Crystal structure of mutant S188A of photosynthetic glyceraldehyde-3-phosphate dehydrogenase A4 isoform, complexed with NADP

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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