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1gg0

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Revision as of 06:16, 3 January 2018

CRYSTAL STRUCTURE ANALYSIS OF KDOP SYNTHASE AT 3.0 A

Structural highlights

1gg0 is a 1 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:	1d9e, 1gg1
Activity:	3-deoxy-8-phosphooctulonate synthase, with EC number 2.5.1.55
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[KDSA_ECOLI] Synthesis of KDO 8-P which is required for lipid A maturation and cellular growth.[HAMAP-Rule:MF_00056]

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

The crystal structure of 3-deoxy-d-manno-octulosonate-8-phosphate synthase (KDOPS) from Escherichia coli was determined by molecular replacement using coordinates given to us by Radaev and co-workers prior to publication. The KDOPS crystals reported by Radaev et al. were grown in the presence of 1.4 M (NH(4))(2)SO(4) and 0.4 M (K/H)(3)PO(4). They are in the cubic space group I23 (a=228.6 A) with a tetramer in the asymmetric unit; the structure has been refined with data to 2.4 A. Our crystals of E. coli KDOPS, grown in 24 % (w/v) polyethylene glycol (PEG) 1500 in the presence of the substrates, 2-phosphoenolpyruvate (PEP) and d-arabinose-5-phosphate (A5P), are also in space group I23 (a=118.2 A), with one subunit in the asymmetric unit.The medium of crystallization, 1.8 M SO(4)/PO(4) versus 24 % PEG, does not significantly affect the conformation of KDOPS. The inter-monomer contacts in both structures are the same. The beta(8)/alpha(8) loop (residues 246 to 251) situated near the entrance to the active site is not seen in the 229 A structure but can be traced in the 118 A structure.Most significantly, Radaev et al. interpreted two SO(4)/PO(4) sites in the 229 A structure as marking the phosphate positions of the substrates, PEP and A5P, after the precedent of DAHPS. In the 118 A structure the inner of these two SO(4)/PO(4) peaks is present at the same position as in the 229 A structure of KDOPS. The outer phosphate peak in the 118 A KDOPS is 3.7 A from the outer SO(4)/PO(4) peak in the 229 A structure and is within hydrogen bonding distance of Arg63 of the same subunit and Arg120 of another subunit. Based on the precedent of the d-erythrose-4-phosphate (E4P) modeled in the active site of DAHPS, we have modeled PEP and A5P in KDOPS and compared the coordination of PEP and A5P in KDOPS with that of PEP and E4P in DAHPS.

3-Deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli. Model of binding of phosphoenolpyruvate and D-arabinose-5-phosphate.,Wagner T, Kretsinger RH, Bauerle R, Tolbert WD J Mol Biol. 2000 Aug 11;301(2):233-8. PMID:10926505^[1]

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

References

↑ Wagner T, Kretsinger RH, Bauerle R, Tolbert WD. 3-Deoxy-D-manno-octulosonate-8-phosphate synthase from Escherichia coli. Model of binding of phosphoenolpyruvate and D-arabinose-5-phosphate. J Mol Biol. 2000 Aug 11;301(2):233-8. PMID:10926505 doi:10.1006/jmbi.2000.3956

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/1gg0"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE ANALYSIS OF KDOP SYNTHASE AT 3.0 A==
 <StructureSection load='1gg0' size='340' side='right' caption='[[1gg0]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1d9e|1d9e]], [[1gg1|1gg1]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/3-deoxy-8-phosphooctulonate_synthase 3-deoxy-8-phosphooctulonate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.55 2.5.1.55] </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=1gg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gg0 OCA], [http://pdbe.org/1gg0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gg0 RCSB], [http://www.ebi.ac.uk/pdbsum/1gg0 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=1gg0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gg0 OCA], [http://pdbe.org/1gg0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1gg0 RCSB], [http://www.ebi.ac.uk/pdbsum/1gg0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1gg0 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/gg/1gg0_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gg/1gg0_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 29: / Line 30: @@
 </div>
 <div class="pdbe-citations 1gg0" style="background-color:#fffaf0;"></div>
-==See Also==
-*[[Kdo-8-phosphate synthase|Kdo-8-phosphate synthase]]
 == References ==
 <references/>

1gg0

From Proteopedia

Revision as of 06:16, 3 January 2018

CRYSTAL STRUCTURE ANALYSIS OF KDOP SYNTHASE AT 3.0 A

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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