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| | ==Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate== | | ==Granulibacter bethesdensis allophanate hydrolase co-crystallized with malonate== |
| - | <StructureSection load='4gys' size='340' side='right' caption='[[4gys]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='4gys' size='340' side='right'caption='[[4gys]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4gys]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Grabc Grabc]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GYS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GYS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4gys]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Granulibacter_bethesdensis_CGDNIH1 Granulibacter bethesdensis CGDNIH1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GYS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GYS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4gyr|4gyr]]</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=4gys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gys OCA], [https://pdbe.org/4gys PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gys RCSB], [https://www.ebi.ac.uk/pdbsum/4gys PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gys ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GbCGDNIH1_1744 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=391165 GRABC])</td></tr>
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| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Allophanate_hydrolase Allophanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.54 3.5.1.54] </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=4gys FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gys OCA], [http://pdbe.org/4gys PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gys RCSB], [http://www.ebi.ac.uk/pdbsum/4gys PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gys ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/Q0BRB0_GRABC Q0BRB0_GRABC] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Allophanate hydrolase]] | + | [[Category: Granulibacter bethesdensis CGDNIH1]] |
| - | [[Category: Grabc]] | + | [[Category: Large Structures]] |
| - | [[Category: Lin, Y]] | + | [[Category: Lin Y]] |
| - | [[Category: Maurice, M St]] | + | [[Category: St Maurice M]] |
| - | [[Category: Amidase signature family enzyme]]
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| - | [[Category: Hydrolase]]
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| Structural highlights
Function
Q0BRB0_GRABC
Publication Abstract from PubMed
Allophanate hydrolase (AH) catalyzes the hydrolysis of allophanate, an intermediate in atrazine degradation and urea catabolism pathways, to NH(3) and CO(2). AH belongs to the amidase signature family, which is characterized by a conserved block of 130 amino acids rich in Gly and Ser and a Ser-cis-Ser-Lys catalytic triad. In this study, the first structures of AH from Granulibacter bethesdensis were determined, with and without the substrate analogue malonate, to 2.2 and 2.8 A, respectively. The structures confirm the identity of the catalytic triad residues and reveal an altered dimerization interface that is not conserved in the amidase signature family. The structures also provide insights into previously unrecognized substrate specificity determinants in AH. Two residues, Tyr(299) and Arg(307), are within hydrogen bonding distance of a carboxylate moiety of malonate. Both Tyr(299) and Arg(307) were mutated, and the resulting modified enzymes revealed >3 order of magnitude reductions in both catalytic efficiency and substrate stringency. It is proposed that Tyr(299) and Arg(307) serve to anchor and orient the substrate for attack by the catalytic nucleophile, Ser(172). The structure further suggests the presence of a unique C-terminal domain in AH. While this domain is conserved, it does not contribute to catalysis or to the structural integrity of the core domain, suggesting that it may play a role in mediating transient and specific interactions with the urea carboxylase component of urea amidolyase. Analysis of the AH active site architecture offers new insights into common determinants of catalysis and specificity among divergent members of the amidase signature family.
The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family.,Lin Y, St Maurice M Biochemistry. 2013 Jan 29;52(4):690-700. doi: 10.1021/bi301242m. Epub 2013 Jan, 18. PMID:23282241[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lin Y, St Maurice M. The Structure of Allophanate Hydrolase from Granulibacter bethesdensis Provides Insights into Substrate Specificity in the Amidase Signature Family. Biochemistry. 2013 Jan 29;52(4):690-700. doi: 10.1021/bi301242m. Epub 2013 Jan, 18. PMID:23282241 doi:http://dx.doi.org/10.1021/bi301242m
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