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6azs

From Proteopedia

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Structural and biochemical characterization of a non-canonical biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841

Structural highlights

6azs is a 4 chain structure with sequence from Rhizobium leguminosarum bv. viciae 3841. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.59Å
Ligands:	, , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BIUH_RHIL3 Involved in the degradation of cyanuric acid, an intermediate in the degradation of s-triazide herbicides such as atrazine (PubMed:21897878). Catalyzes the hydrolysis of biuret to urea-1-carboxylate (allophanate) and ammonia (PubMed:21897878, PubMed:29425231). The substrate, biuret, is formed by the spontaneous decarboxylation of carboxybiuret (PubMed:21897878).^[1] ^[2]

Publication Abstract from PubMed

Biuret deamination is an essential step in cyanuric acid mineralization. In the well-studied atrazine degrading bacterium Pseudomonas sp. strain ADP, the amidase AtzE catalyzes this step. However, Rhizobium leguminosarum bv. viciae 3841 uses an unrelated cysteine hydrolase, BiuH, instead. Herein, structures of BiuH, BiuH with bound inhibitor and variants of BiuH are reported. The substrate is bound in the active site by a hydrogen bonding network that imparts high substrate specificity. The structure of the inactive Cys175Ser BiuH variant with substrate bound in the active site revealed that an active site cysteine (Cys175), aspartic acid (Asp36) and lysine (Lys142) form a catalytic triad, which is consistent with biochemical studies of BiuH variants. Finally, molecular dynamics simulations highlighted the presence of three channels from the active site to the enzyme surface: a persistent tunnel gated by residues Val218 and Gln215 forming a potential substrate channel and two smaller channels formed by Val28 and a mobile loop (including residues Phe41, Tyr47 and Met51) that may serve as channels for co-product (ammonia) or co-substrate (water).

Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841.,Esquirol L, Peat TS, Wilding M, Lucent D, French NG, Hartley CJ, Newman J, Scott C PLoS One. 2018 Feb 9;13(2):e0192736. doi: 10.1371/journal.pone.0192736., eCollection 2018. PMID:29425231^[3]

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

References

↑ Cameron SM, Durchschein K, Richman JE, Sadowsky MJ, Wackett LP. A New Family of Biuret Hydrolases Involved in S-Triazine Ring Metabolism. ACS Catal. 2011 Aug 1;2011(1):1075-1082. PMID:21897878 doi:10.1021/cs200295n
↑ Esquirol L, Peat TS, Wilding M, Lucent D, French NG, Hartley CJ, Newman J, Scott C. Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841. PLoS One. 2018 Feb 9;13(2):e0192736. doi: 10.1371/journal.pone.0192736., eCollection 2018. PMID:29425231 doi:http://dx.doi.org/10.1371/journal.pone.0192736
↑ Esquirol L, Peat TS, Wilding M, Lucent D, French NG, Hartley CJ, Newman J, Scott C. Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841. PLoS One. 2018 Feb 9;13(2):e0192736. doi: 10.1371/journal.pone.0192736., eCollection 2018. PMID:29425231 doi:http://dx.doi.org/10.1371/journal.pone.0192736

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/6azs"

@@ Line 3: / Line 3: @@
 <StructureSection load='6azs' size='340' side='right'caption='[[6azs]], [[Resolution|resolution]] 1.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6azs]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AZS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6AZS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6azs]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhizobium_leguminosarum_bv._viciae_3841 Rhizobium leguminosarum bv. viciae 3841]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6AZS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6AZS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=C5S:N-formyl-D-aspartic+acid'>C5S</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 1.59&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6azs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6azs OCA], [http://pdbe.org/6azs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6azs RCSB], [http://www.ebi.ac.uk/pdbsum/6azs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6azs ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BTB:2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>BTB</scene>, <scene name='pdbligand=C5S:N-formyl-D-aspartic+acid'>C5S</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=6azs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6azs OCA], [https://pdbe.org/6azs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6azs RCSB], [https://www.ebi.ac.uk/pdbsum/6azs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6azs ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/BIUH_RHIL3 BIUH_RHIL3] Involved in the degradation of cyanuric acid, an intermediate in the degradation of s-triazide herbicides such as atrazine (PubMed:21897878). Catalyzes the hydrolysis of biuret to urea-1-carboxylate (allophanate) and ammonia (PubMed:21897878, PubMed:29425231). The substrate, biuret, is formed by the spontaneous decarboxylation of carboxybiuret (PubMed:21897878).<ref>PMID:21897878</ref> <ref>PMID:29425231</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 24: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Esquirol, L]]
+[[Category: Rhizobium leguminosarum bv. viciae 3841]]
-[[Category: Newman, J]]
+[[Category: Esquirol L]]
-[[Category: Peat, T S]]
+[[Category: Newman J]]
-[[Category: Scott, C]]
+[[Category: Peat TS]]
-[[Category: Hydrolase-hydrolase inhibitor complex]]
+[[Category: Scott C]]
-[[Category: S-triazine]]
-[[Category: Xenobiotic]]

6azs

From Proteopedia

Current revision

Structural and biochemical characterization of a non-canonical biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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