2zuk: Difference between revisions

Latest revision as of 13:55, 1 November 2023

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam (different binding mode)

Structural highlights

2zuk 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.
Method:	X-ray diffraction, Resolution 2.41Å
Ligands:	ICC, PLP
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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:https://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:https://dx.doi.org/10.1021/bi801574p

Proteopedia Page Contributors and Editors (what is this?)

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

[2] 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]

[2]

@@ Line 3: / Line 3: @@
 <StructureSection load='2zuk' size='340' side='right'caption='[[2zuk]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
 == 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://proteopedia.org/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" id="ligandDat"><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]] 2.41&#8491;</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://proteopedia.org/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>
+== 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 34: @@
 </StructureSection>
 [[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]]

2zuk: Difference between revisions

Latest revision as of 13:55, 1 November 2023

The crystal structure of alpha-amino-epsilon-caprolactam racemase from Achromobacter obae complexed with epsilon caprolactam (different binding mode)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

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