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1k1e

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Revision as of 23:43, 10 September 2015

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Structural highlights

1k1e is a 12 chain structure with sequence from Haein. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , ,
Related:	1j8d
Gene:	HI1679 (HAEIN)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[KDSC_HAEIN] Involved in the biosynthesis of lipopolysaccharides (LPSs), but is not essential. Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) 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

The crystal structure of the YrbI protein from Haemophilus influenzae (HI1679) was determined at a 1.67-A resolution. The function of the protein had not been assigned previously, and it is annotated as hypothetical in sequence databases. The protein exhibits the alpha/beta-hydrolase fold (also termed the Rossmann fold) and resembles most closely the fold of the L-2-haloacid dehalogenase (HAD) superfamily. Following this observation, a detailed sequence analysis revealed remote homology to two members of the HAD superfamily, the P-domain of Ca(2+) ATPase and phosphoserine phosphatase. The 19-kDa chains of HI1679 form a tetramer both in solution and in the crystalline form. The four monomers are arranged in a ring such that four beta-hairpin loops, each inserted after the first beta-strand of the core alpha/beta-fold, form an eight-stranded barrel at the center of the assembly. Four active sites are located at the subunit interfaces. Each active site is occupied by a cobalt ion, a metal used for crystallization. The cobalt is octahedrally coordinated to two aspartate side-chains, a backbone oxygen, and three solvent molecules, indicating that the physiological metal may be magnesium. HI1679 hydrolyzes a number of phosphates, including 6-phosphogluconate and phosphotyrosine, suggesting that it functions as a phosphatase in vivo. The physiological substrate is yet to be identified; however the location of the gene on the yrb operon suggests involvement in sugar metabolism.

From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase.,Parsons JF, Lim K, Tempczyk A, Krajewski W, Eisenstein E, Herzberg O Proteins. 2002 Mar 1;46(4):393-404. PMID:11835514^[2]

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

References

↑ Wu J, Woodard RW. Escherichia coli YrbI is 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase. J Biol Chem. 2003 May 16;278(20):18117-23. Epub 2003 Mar 14. PMID:12639950 doi:http://dx.doi.org/10.1074/jbc.M301983200
↑ Parsons JF, Lim K, Tempczyk A, Krajewski W, Eisenstein E, Herzberg O. From structure to function: YrbI from Haemophilus influenzae (HI1679) is a phosphatase. Proteins. 2002 Mar 1;46(4):393-404. PMID:11835514

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/1k1e"

@@ Line 2: / Line 2: @@
 <StructureSection load='1k1e' size='340' side='right' caption='[[1k1e]], [[Resolution|resolution]] 1.67&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1k1e]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae_rd_kw20 Haemophilus influenzae rd kw20]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K1E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1k1e]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Haein Haein]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K1E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1K1E FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1j8d|1j8d]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HI1679 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 Haemophilus influenzae Rd KW20])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">HI1679 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=71421 HAEIN])</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=1k1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1e OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1k1e RCSB], [http://www.ebi.ac.uk/pdbsum/1k1e 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=1k1e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k1e OCA], [http://pdbe.org/1k1e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1k1e RCSB], [http://www.ebi.ac.uk/pdbsum/1k1e PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/KDOP_HAEIN KDOP_HAEIN]] Involved in the biosynthesis of lipopolysaccharides (LPSs), but is not essential. Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.<ref>PMID:12639950</ref>
+[[http://www.uniprot.org/uniprot/KDSC_HAEIN KDSC_HAEIN]] Involved in the biosynthesis of lipopolysaccharides (LPSs), but is not essential. Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate.<ref>PMID:12639950</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1k1e" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Haemophilus influenzae rd kw20]]
+[[Category: Haein]]
 [[Category: Herzberg, O]]
 [[Category: Lim, K]]

1k1e

From Proteopedia

Revision as of 23:43, 10 September 2015

Structure Of the cobalt-bound form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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