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2wym

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Structure of a metallo-b-lactamase

Structural highlights

2wym is a 6 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.6Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ULAG_ECOLI Probably catalyzes the hydrolysis of L-ascorbate-6-P into 3-keto-L-gulonate-6-P. Is essential for L-ascorbate utilization under anaerobic conditions. Also shows phosphodiesterase activity, hydrolyzing phosphodiester bond in the artificial chromogenic substrate bis-p-nitrophenyl phosphate (bis-pNPP).^[1] ^[2]

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 ulaG gene, located in the ula regulon, is crucial for the catabolism of l-ascorbate under anaerobic conditions and it has been proposed to encode for the putative l-ascorbate-6-P lactonase. The ulaG gene is widespread among eubacteria, including human commensal and pathogenic genera such as Escherichia, Shigella, Klebsiella and Salmonella. Here, we report the three-dimensional structures of the apoenzyme and Mn(2+) holoenzyme of UlaG from E. coli to 2.6 A resolution, determined using single-wavelength anomalous diffraction phasing and molecular replacement, respectively. The structures reveal a highly specialized metallo-beta-lactamase-like fold derived from an ancient structural template that was involved in RNA maturation and DNA repair. This fold has a novel quaternary architecture consisting of a hexameric ring formed by a trimer of UlaG dimers. A mononuclear Mn(2)(+)-binding site resides at the core of the active site, which displays micromolar affinity for Mn(2+) and a distorted trigonal bipyramidal coordination. The active site Mn(2+) ion can be replaced by Co(2+) or Zn(2+), but not by Fe(3+). We further show that the Mn(2+) or Co(2)(+)-loaded enzyme exhibits lactonase activity towards l-ascorbate 6-P, thereby providing the first direct evidence of its catalytic role in the L-ascorbate catabolic pathway. Guided by the structural homology, we show that UlaG is able to cleave phosphodiester linkages in cyclic nucleotides, suggesting that the conservation of the fold and of the key catalytic residues allows for the evolutionary acquisition of substrate specificity for novel but related substrates.

Molecular architecture of the Mn2+-dependent lactonase UlaG reveals an RNase-like metallo-beta-lactamase fold and a novel quaternary structure.,Garces F, Fernandez FJ, Montella C, Penya-Soler E, Prohens R, Aguilar J, Baldoma L, Coll M, Badia J, Vega MC J Mol Biol. 2010 May 21;398(5):715-29. Epub 2010 Mar 30. PMID:20359483^[3]

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

References

↑ Zhang Z, Aboulwafa M, Smith MH, Saier MH Jr. The ascorbate transporter of Escherichia coli. J Bacteriol. 2003 Apr;185(7):2243-50. PMID:12644495
↑ Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF. Enzyme genomics: Application of general enzymatic screens to discover new enzymes. FEMS Microbiol Rev. 2005 Apr;29(2):263-79. PMID:15808744 doi:S0168-6445(05)00004-5
↑ Garces F, Fernandez FJ, Montella C, Penya-Soler E, Prohens R, Aguilar J, Baldoma L, Coll M, Badia J, Vega MC. Molecular architecture of the Mn2+-dependent lactonase UlaG reveals an RNase-like metallo-beta-lactamase fold and a novel quaternary structure. J Mol Biol. 2010 May 21;398(5):715-29. Epub 2010 Mar 30. PMID:20359483 doi:10.1016/j.jmb.2010.03.041

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/2wym"

@@ Line 1: / Line 1: @@
-==STRUCTURE OF A METALLO-B-LACTAMASE==
+==Structure of a metallo-b-lactamase==
-<StructureSection load='2wym' size='340' side='right' caption='[[2wym]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+<StructureSection load='2wym' size='340' side='right'caption='[[2wym]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2wym]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2WYM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2wym]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2WYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WYM FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.6&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FLC:CITRATE+ANION'>FLC</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2wyl|2wyl]]</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=2wym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wym OCA], [https://pdbe.org/2wym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wym RCSB], [https://www.ebi.ac.uk/pdbsum/2wym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wym ProSAT]</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=2wym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wym OCA], [http://pdbe.org/2wym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2wym RCSB], [http://www.ebi.ac.uk/pdbsum/2wym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2wym ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ULAG_ECOLI ULAG_ECOLI]] Probably catalyzes the hydrolysis of L-ascorbate-6-P into 3-keto-L-gulonate-6-P. Is essential for L-ascorbate utilization under anaerobic conditions. Also shows phosphodiesterase activity, hydrolyzing phosphodiester bond in the artificial chromogenic substrate bis-p-nitrophenyl phosphate (bis-pNPP).<ref>PMID:12644495</ref> <ref>PMID:15808744</ref>
+[https://www.uniprot.org/uniprot/ULAG_ECOLI ULAG_ECOLI] Probably catalyzes the hydrolysis of L-ascorbate-6-P into 3-keto-L-gulonate-6-P. Is essential for L-ascorbate utilization under anaerobic conditions. Also shows phosphodiesterase activity, hydrolyzing phosphodiester bond in the artificial chromogenic substrate bis-p-nitrophenyl phosphate (bis-pNPP).<ref>PMID:12644495</ref> <ref>PMID:15808744</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/2wym_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/2wym_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
-[[Category: Aguilar, J]]
+[[Category: Large Structures]]
-[[Category: Badia, J]]
+[[Category: Aguilar J]]
-[[Category: Baldoma, L]]
+[[Category: Badia J]]
-[[Category: Coll, M]]
+[[Category: Baldoma L]]
-[[Category: Fernandez, F J]]
+[[Category: Coll M]]
-[[Category: Garces, F]]
+[[Category: Fernandez FJ]]
-[[Category: Penya-Soler, E]]
+[[Category: Garces F]]
-[[Category: Vega, M C]]
+[[Category: Penya-Soler E]]
-[[Category: Hydrolase]]
+[[Category: Vega MC]]

2wym

From Proteopedia

Current revision

Structure of a metallo-b-lactamase

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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