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1m5w

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Revision as of 07:56, 31 January 2018

1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate

Structural highlights

1m5w is a 8 chain structure with sequence from "bacillus_coli"_migula_1895 "bacillus coli" migula 1895. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1ho1, 1ho4
Gene:	PDXJ ("Bacillus coli" Migula 1895)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[PDXJ_ECOLI] Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate.^[1]

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

We report the 1.96 A crystal structure of pyridoxine 5'-phosphate synthase (PdxJ) in complex with 1-deoxy-D-xylulose phosphate (dXP). The octameric enzyme possesses eight distinct binding sites, and three different binding states are observed. The observation of these three states supports a mechanism in which precise conformational changes of a peptide loop and groups of active site residues modulate binding and specificity. The differences in protein conformation when one or two substrates are bound can be correlated with a condensation mechanism that leads productively to the formation of pyridoxine 5'-phosphate (PNP). "Snapshots" of the progression from the apo form to a singly occupied "transitional binding" state and, subsequently, to a fully occupied, reactive state are revealed and indicate how the enzyme structure can be related to a plausible catalytic mechanism and, moreover, to favorable energetics of reaction.

Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate.,Yeh JI, Du S, Pohl E, Cane DE Biochemistry. 2002 Oct 1;41(39):11649-57. PMID:12269807^[2]

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

References

↑ Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS. Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein. FEBS Lett. 1999 Apr 16;449(1):45-8. PMID:10225425
↑ Yeh JI, Du S, Pohl E, Cane DE. Multistate binding in pyridoxine 5'-phosphate synthase: 1.96 A crystal structure in complex with 1-deoxy-D-xylulose phosphate. Biochemistry. 2002 Oct 1;41(39):11649-57. PMID:12269807

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1m5w"

@@ Line 1: / Line 1: @@
 ==1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate==
 <StructureSection load='1m5w' size='340' side='right' caption='[[1m5w]], [[Resolution|resolution]] 1.96&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ho1|1ho1]], [[1ho4|1ho4]]</td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PDXJ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=1m5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5w OCA], [http://pdbe.org/1m5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m5w RCSB], [http://www.ebi.ac.uk/pdbsum/1m5w PDBsum]</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=1m5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m5w OCA], [http://pdbe.org/1m5w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m5w RCSB], [http://www.ebi.ac.uk/pdbsum/1m5w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m5w ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m5/1m5w_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m5/1m5w_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>

1m5w

From Proteopedia

Revision as of 07:56, 31 January 2018

1.96 A Crystal Structure of Pyridoxine 5'-Phosphate Synthase in Complex with 1-deoxy-D-xylulose phosphate

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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