3dxv: Difference between revisions

Revision as of 07:02, 19 August 2020

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae

Structural highlights

3dxv is a 2 chain structure with sequence from 'achromobacter obae'. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	PLP
Related:	3dxw
Activity:	2-aminohexano-6-lactam racemase, with EC number 5.1.1.15
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Alpha-amino-epsilon-caprolactam (ACL) racemase (ACLR) from Achromobacter obae catalyzes the interconversion of l- and d-ACL. ACLR belongs to the fold-type I group of pyridoxal 5'-phosphate (PLP) dependent enzymes. In this study, the first crystal structures of a fold-type I racemase are solved for the native form and epsilon-caprolactam-complexed form of ACLR at 2.21 and 2.40 A resolution, respectively. Based on the location of epsilon-caprolactam in the complex structure, the substrate-binding site is assigned between Trp49 and Tyr137. The carboxyl group of Asp210 is a reasonable candidate that recognizes the nitrogen atom of a lactam or amide in the substrate. Based on a structural comparison with fold-type III alanine racemase, Tyr137 is potentially the acid/base catalytic residue that is essential for the two-base racemization mechanism. The overall structure of ACLR is similar to that of fold-type I enzymes. A structural comparison with these enzymes explains the different reaction specificities.

The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae.,Okazaki S, Suzuki A, Mizushima T, Kawano T, Komeda H, Asano Y, Yamane T Biochemistry. 2009 Feb 10;48(5):941-50. PMID:19146406^[1]

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

References

↑ Okazaki S, Suzuki A, Mizushima T, Kawano T, Komeda H, Asano Y, Yamane T. The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae. Biochemistry. 2009 Feb 10;48(5):941-50. PMID:19146406 doi:https://dx.doi.org/10.1021/bi801574p

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OCA

[1] Okazaki S, Suzuki A, Mizushima T, Kawano T, Komeda H, Asano Y, Yamane T. The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae. Biochemistry. 2009 Feb 10;48(5):941-50. PMID:19146406 doi:https://dx.doi.org/10.1021/bi801574p

[1]

@@ Line 1: / Line 1: @@
 ==The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae==
-<StructureSection load='3dxv' size='340' side='right' caption='[[3dxv]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
+<StructureSection load='3dxv' size='340' side='right'caption='[[3dxv]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3dxv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'achromobacter_obae' 'achromobacter obae']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DXV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DXV FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3dxv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/'achromobacter_obae' 'achromobacter obae']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DXV OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3DXV FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dxw|3dxw]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-aminohexano-6-lactam_racemase 2-aminohexano-6-lactam racemase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.15 5.1.1.15] </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=3dxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dxv OCA], [http://pdbe.org/3dxv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dxv RCSB], [http://www.ebi.ac.uk/pdbsum/3dxv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dxv ProSAT]</span></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=3dxv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dxv OCA], [http://pdbe.org/3dxv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dxv RCSB], [http://www.ebi.ac.uk/pdbsum/3dxv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dxv ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 34: / Line 34: @@
 [[Category: Achromobacter obae]]
 [[Category: 2-aminohexano-6-lactam racemase]]
+[[Category: Large Structures]]
 [[Category: Asano, Y]]
 [[Category: Komeda, H]]

3dxv: Difference between revisions

Revision as of 07:02, 19 August 2020

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

References

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