2ip4

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(Difference between revisions)

Revision as of 07:55, 4 July 2018

Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8

Structural highlights

2ip4 is a 2 chain structure with sequence from Thet8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	TTHA0811 (THET8)
Activity:	Phosphoribosylamine--glycine ligase, with EC number 6.3.4.13
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

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

Glycinamide ribonucleotide synthetase (GAR-syn, PurD) catalyses the second reaction of the purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine and ATP to glycinamide ribonucleotide (GAR), ADP and Pi. In the present study, crystal structures of GAR-syn's from Thermus thermophilus, Geobacillus kaustophilus and Aquifex aeolicus were determined in apo forms. Crystal structures in ligand-bound forms were also determined for G. kaustophilus and A. aeolicus proteins. In general, overall structures of GAR-syn's are similar to each other. However, the orientations of the B domains are varied among GAR-syn's and the MD simulation suggested the mobility of the B domain. Furthermore, it was demonstrated that the B loop in the B domain fixes the position of the beta- and gamma- phosphate groups of the bound ATP. The structures of GAR-syn's and the bound ligands were compared with each other in detail, and structures of GAR-syn's with full ligands, as well as the possible reaction mechanism, were proposed.

Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria.,Sampei G, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G J Biochem. 2010 Oct;148(4):429-38. Epub 2010 Aug 16. PMID:20716513^[1]

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

References

↑ Sampei G, Baba S, Kanagawa M, Yanai H, Ishii T, Kawai H, Fukai Y, Ebihara A, Nakagawa N, Kawai G. Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria. J Biochem. 2010 Oct;148(4):429-38. Epub 2010 Aug 16. PMID:20716513 doi:10.1093/jb/mvq088

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ip4"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8==
 <StructureSection load='2ip4' size='340' side='right' caption='[[2ip4]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TTHA0811 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Phosphoribosylamine--glycine_ligase Phosphoribosylamine--glycine ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.13 6.3.4.13] </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=2ip4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ip4 OCA], [http://pdbe.org/2ip4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ip4 RCSB], [http://www.ebi.ac.uk/pdbsum/2ip4 PDBsum], [http://www.topsan.org/Proteins/RSGI/2ip4 TOPSAN]</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=2ip4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ip4 OCA], [http://pdbe.org/2ip4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ip4 RCSB], [http://www.ebi.ac.uk/pdbsum/2ip4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ip4 ProSAT], [http://www.topsan.org/Proteins/RSGI/2ip4 TOPSAN]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/2ip4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ip/2ip4_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=2ip4 ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

2ip4

From Proteopedia

Revision as of 07:55, 4 July 2018

Crystal Structure of Glycinamide Ribonucleotide Synthetase from Thermus thermophilus HB8

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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