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| | ==The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam (different binding mode)== | | ==The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam (different binding mode)== |
| - | <StructureSection load='2zuk' size='340' side='right' caption='[[2zuk]], [[Resolution|resolution]] 2.41Å' scene=''> | + | <StructureSection load='2zuk' size='340' side='right'caption='[[2zuk]], [[Resolution|resolution]] 2.41Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2zuk]] 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=2ZUK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ZUK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2zuk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Achromobacter_obae Achromobacter obae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZUK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZUK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ICC:AZEPAN-2-ONE'>ICC</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</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]] 2.41Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3dxv|3dxv]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ICC:AZEPAN-2-ONE'>ICC</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=2zuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zuk OCA], [https://pdbe.org/2zuk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zuk RCSB], [https://www.ebi.ac.uk/pdbsum/2zuk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zuk 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=2zuk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zuk OCA], [http://pdbe.org/2zuk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2zuk RCSB], [http://www.ebi.ac.uk/pdbsum/2zuk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2zuk ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/ACLR_ACHOB ACLR_ACHOB] catalyzes the interconversion of L-alpha-amino-epsilon-caprolactam and D-alpha-amino-epsilon-caprolactam.<ref>PMID:19146406</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Achromobacter obae]] | | [[Category: Achromobacter obae]] |
| - | [[Category: 2-aminohexano-6-lactam racemase]] | + | [[Category: Large Structures]] |
| - | [[Category: Asano, Y]] | + | [[Category: Asano Y]] |
| - | [[Category: Komeda, H]] | + | [[Category: Komeda H]] |
| - | [[Category: Okazaki, S]] | + | [[Category: Okazaki S]] |
| - | [[Category: Suzuki, A]] | + | [[Category: Suzuki A]] |
| - | [[Category: Yamane, T]] | + | [[Category: Yamane T]] |
| - | [[Category: Fold-type1]]
| + | |
| - | [[Category: Isomerase]]
| + | |
| - | [[Category: Pyridoxal phosphate]]
| + | |
| - | [[Category: Pyridoxal-5'-phosphate dependent racemase]]
| + | |
| Structural highlights
Function
ACLR_ACHOB catalyzes the interconversion of L-alpha-amino-epsilon-caprolactam and D-alpha-amino-epsilon-caprolactam.[1]
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[2]
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:http://dx.doi.org/10.1021/bi801574p
- ↑ 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:http://dx.doi.org/10.1021/bi801574p
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