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2yb4

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Structure of an amidohydrolase from Chromobacterium violaceum (EFI target EFI-500202) with bound SO4, no metal

Structural highlights

2yb4 is a 1 chain structure with sequence from Chromobacterium violaceum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

35NBP_CHRVO Hydrolyzes 3',5'-bisphosphonucleosides (pGp, pCp, pUp, and pIp) to nucleoside 5'-phosphate and orthophosphate. Has similar catalytic efficiencies with all the bases. Also shows activity with ribonucleoside 2'-deoxyribonucleoside 3',5'-bisphosphates. Does not show activity with nucleoside 2',5'-bisphosphates.^[1]

Publication Abstract from PubMed

In bacteria, 3',5'-adenosine bisphosphate (pAp) is generated from 3'-phosphoadenosine 5'-phosphosulfate in the sulfate assimilation pathway, and from coenzyme A by the transfer of the phosphopantetheine group to the acyl-carrier protein. pAp is subsequently hydrolyzed to 5'-AMP and orthophosphate, and this reaction has been shown to be important for superoxide stress tolerance. Herein, we report the discovery of the first instance of an enzyme from the amidohydrolase superfamily that is capable of hydrolyzing pAp. Crystal structures of Cv1693 from Chromobacterium violaceum have been determined to a resolution of 1.9 A with AMP and orthophosphate bound in the active site. The enzyme has a trinuclear metal center in the active site with three Mn2+ ions. This enzyme (Cv1693) belongs to the Cluster of Orthologous Groups cog0613 from the polymerase and histidinol phosphatase family of enzymes. The values of kcat and kcat/Km for the hydrolysis of pAp are 22 s-1 and 1.4 x 106 M-1 s-1, respectively. The enzyme is promiscuous and is able to hydrolyze other 3',5'-bisphosphonucleotides (pGp, pCp, pUp, and pIp) and 2'-deoxynucleotides with comparable catalytic efficiency. The enzyme is capable of hydrolyzing short oligonucleotides (pdA)5, albeit at rates much lower than that of pAp. Enzymes from two other enzyme families have previously been found to hydrolyze pAp at physiologically significant rates. These enzymes include CysQ from Escherichia coli (cog1218) and YtqI/NrnA from Bacillus subtilis (cog0618). Identification of the functional homologues to the experimentally verified pAp phosphatases from cog0613, cog1218, and cog0618 suggests that there is relatively little overlap of enzymes with this function in sequenced bacterial genomes.

Prospecting for Unannotated Enzymes: Discovery of a 3',5'-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily.,Cummings JA, Vetting M, Ghodge SV, Xu C, Hillerich B, Seidel RD, Almo SC, Raushel FM Biochemistry. 2014 Jan 13. PMID:24401123^[2]

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

References

↑ Cummings JA, Vetting M, Ghodge SV, Xu C, Hillerich B, Seidel RD, Almo SC, Raushel FM. Prospecting for Unannotated Enzymes: Discovery of a 3',5'-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily. Biochemistry. 2014 Jan 13. PMID:24401123 doi:http://dx.doi.org/10.1021/bi401640r
↑ Cummings JA, Vetting M, Ghodge SV, Xu C, Hillerich B, Seidel RD, Almo SC, Raushel FM. Prospecting for Unannotated Enzymes: Discovery of a 3',5'-Nucleotide Bisphosphate Phosphatase within the Amidohydrolase Superfamily. Biochemistry. 2014 Jan 13. PMID:24401123 doi:http://dx.doi.org/10.1021/bi401640r

1 Structural highlights
2 Function
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/2yb4"

@@ Line 3: / Line 3: @@
 <StructureSection load='2yb4' size='340' side='right'caption='[[2yb4]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2yb4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"chromobacterium_janthinum"_(zopf)_ford_1927 "chromobacterium janthinum" (zopf) ford 1927]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YB4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2yb4]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chromobacterium_violaceum Chromobacterium violaceum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YB4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YB4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2yb1|2yb1]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2yb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yb4 OCA], [https://pdbe.org/2yb4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yb4 RCSB], [https://www.ebi.ac.uk/pdbsum/2yb4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yb4 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/35NBP_CHRVO 35NBP_CHRVO] Hydrolyzes 3',5'-bisphosphonucleosides (pGp, pCp, pUp, and pIp) to nucleoside 5'-phosphate and orthophosphate. Has similar catalytic efficiencies with all the bases. Also shows activity with ribonucleoside 2'-deoxyribonucleoside 3',5'-bisphosphates. Does not show activity with nucleoside 2',5'-bisphosphates.<ref>PMID:24401123</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: Chromobacterium violaceum]]
 [[Category: Large Structures]]
-[[Category: Almo, S C]]
+[[Category: Almo SC]]
-[[Category: Foti, R]]
+[[Category: Foti R]]
-[[Category: Gerlt, J A]]
+[[Category: Gerlt JA]]
-[[Category: Hillerich, B]]
+[[Category: Hillerich B]]
-[[Category: Imker, H J]]
+[[Category: Imker HJ]]
-[[Category: Raushel, F M]]
+[[Category: Raushel FM]]
-[[Category: Seidel, R D]]
+[[Category: Seidel RD]]
-[[Category: Toro, R]]
+[[Category: Toro R]]
-[[Category: Vetting, M W]]
+[[Category: Vetting MW]]
-[[Category: Zencheck, W D]]
+[[Category: Zencheck WD]]
-[[Category: Cog0613]]
-[[Category: Enzyme function initiative]]
-[[Category: Hydrolase]]

2yb4

From Proteopedia

Current revision

Structure of an amidohydrolase from Chromobacterium violaceum (EFI target EFI-500202) with bound SO4, no metal

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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