1j8d

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[[Image:1j8d.jpg|left|200px]]<br /><applet load="1j8d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1j8d, resolution 2.3&Aring;" />
 
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'''Structure Of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)'''<br />
 
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==Overview==
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==Structure Of the metal-free form of the deoxy-D-mannose-octulosonate 8-phosphate phosphatase (YrbI) From Haemophilus Influenzae (HI1679)==
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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.
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<StructureSection load='1j8d' size='340' side='right'caption='[[1j8d]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1j8d]] is a 4 chain structure with sequence from [https://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=1J8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1J8D FirstGlance]. <br>
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1J8D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae] with <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J8D OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1j8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j8d OCA], [https://pdbe.org/1j8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1j8d RCSB], [https://www.ebi.ac.uk/pdbsum/1j8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1j8d ProSAT]</span></td></tr>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11835514 11835514]
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</table>
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[[Category: Haemophilus influenzae]]
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== Function ==
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[[Category: Single protein]]
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[https://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>
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[[Category: Herzberg, O.]]
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== Evolutionary Conservation ==
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[[Category: Lim, K.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: S2F, Structure 2.Function Project.]]
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Check<jmol>
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[[Category: GOL]]
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<jmolCheckbox>
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[[Category: hi1679]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/j8/1j8d_consurf.spt"</scriptWhenChecked>
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[[Category: kdo 8-p phosphatase]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: s2f]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: structural genomics]]
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</jmolCheckbox>
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[[Category: structure 2 function project]]
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</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=1j8d ConSurf].
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<div style="clear:both"></div>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:19:52 2008''
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Haemophilus influenzae Rd KW20]]
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[[Category: Large Structures]]
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[[Category: Herzberg O]]
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[[Category: Lim K]]

Current revision

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

PDB ID 1j8d

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