This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2jb1

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

The L-amino acid oxidase from Rhodococcus opacus in complex with L- alanine

Structural highlights

2jb1 is a 2 chain structure with sequence from Rhodococcus opacus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.55Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OXLA_RHOOP Catalyzes an oxidative deamination of basic, hydrophobic and aromatic L-amino acids, thus producing hydrogen peroxide that may contribute to the diverse toxic effects of this enzyme (Ref.1). Is active on most L-amino acid (39 on 43 tested) with the exception of L-Thr, L-Pro, and L-Gly (Ref.1).[PROSITE-ProRule:PRU00648]

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

l-Amino acid oxidase from Rhodococcus opacus (roLAAO) is classified as a member of the GR(2)-family of flavin-dependent oxidoreductases according to a highly conserved sequence motif for the cofactor binding. The monomer of the homodimeric enzyme consists of three well-defined domains: the FAD-binding domain corresponding to a general topology throughout the whole GR(2)-family; a substrate-binding domain with almost the same topology as the snake venom LAAO and a helical domain exclusively responsible for the unusual dimerisation mode of the enzyme and not found in other members of the family so far. We describe here high-resolution structures of the binary complex of protein and cofactor as well as the ternary complexes of protein, cofactor and ligands. This structures in addition to the structural knowledge of snake venom LAAO and DAAO from yeast and pig kidney permit more insight into different steps in the reaction mechanism of this class of enzymes. There is strong evidence for hydride transfer as the mechanism of dehydrogenation. This mechanism appears to be uncommon in a sense that the chemical transformation can proceed efficiently without the involvement of amino acid functional groups. Most groups present at the active site are involved in substrate recognition, binding and fixation, i.e. they direct the trajectory of the interacting orbitals. In this mode of catalysis orbital steering/interactions are the predominant factors for the chemical step(s). A mirror-symmetrical relationship between the two substrate-binding sites of d and l-amino acid oxidases is observed which facilitates enantiomeric selectivity while preserving a common arrangement of the residues in the active site. These results are of general relevance for the mechanism of flavoproteins and lead to the proposal of a common dehydrogenation step in the mechanism for l and d-amino acid oxidases.

The structure of a bacterial L-amino acid oxidase from Rhodococcus opacus gives new evidence for the hydride mechanism for dehydrogenation.,Faust A, Niefind K, Hummel W, Schomburg D J Mol Biol. 2007 Mar 16;367(1):234-48. Epub 2006 Dec 1. PMID:17234209^[1]

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

References

↑ Faust A, Niefind K, Hummel W, Schomburg D. The structure of a bacterial L-amino acid oxidase from Rhodococcus opacus gives new evidence for the hydride mechanism for dehydrogenation. J Mol Biol. 2007 Mar 16;367(1):234-48. Epub 2006 Dec 1. PMID:17234209 doi:http://dx.doi.org/10.1016/j.jmb.2006.11.071

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2jb1"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2jb1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodococcus_opacus Rhodococcus opacus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JB1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JB1 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</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]] 1.55&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jae|2jae]], [[2jb2|2jb2]], [[2jb3|2jb3]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/L-amino-acid_oxidase L-amino-acid oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.2 1.4.3.2] </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=2jb1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jb1 OCA], [https://pdbe.org/2jb1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jb1 RCSB], [https://www.ebi.ac.uk/pdbsum/2jb1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jb1 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/OXLA_RHOOP OXLA_RHOOP] Catalyzes an oxidative deamination of basic, hydrophobic and aromatic L-amino acids, thus producing hydrogen peroxide that may contribute to the diverse toxic effects of this enzyme (Ref.1). Is active on most L-amino acid (39 on 43 tested) with the exception of L-Thr, L-Pro, and L-Gly (Ref.1).[PROSITE-ProRule:PRU00648]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 36: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: L-amino-acid oxidase]]
 [[Category: Large Structures]]
 [[Category: Rhodococcus opacus]]
-[[Category: Faust, A]]
+[[Category: Faust A]]
-[[Category: Hummel, W]]
+[[Category: Hummel W]]
-[[Category: Niefind, K]]
+[[Category: Niefind K]]
-[[Category: Schomburg, D]]
+[[Category: Schomburg D]]
-[[Category: Dimerisation mode]]
-[[Category: Fad containing]]
-[[Category: Flavoenzyme]]
-[[Category: Gr2-family]]
-[[Category: Hydride transfer mechanism]]
-[[Category: L-amino acid oxidase]]
-[[Category: Oxidoreductase]]
-[[Category: Reduced fad]]

2jb1

From Proteopedia

Current revision

The L-amino acid oxidase from Rhodococcus opacus in complex with L- alanine

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox