1c0i

From Proteopedia

(Difference between revisions)

Current revision

CRYSTAL STRUCTURE OF D-AMINO ACID OXIDASE IN COMPLEX WITH TWO ANTHRANYLATE MOLECULES

Structural highlights

1c0i is a 1 chain structure with sequence from Rhodotorula toruloides. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OXDA_RHOTO This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.

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

The 3D structure of the flavoprotein D-amino acid oxidase (DAAO) from the yeast Rhodotorula gracilis (RgDAAO) in complex with the competitive inhibitor anthranilate was solved (resolution 1.9A) and structural features relevant for the overall conformation and for catalytic activity are described. The FAD is bound in an elongated conformation in the core of the enzyme. Two anthranilate molecules are found within the active site cavity; one is located in a funnel forming the entrance, and the second is in contact with the flavin. The anchoring of the ligand carboxylate with Arg285 and Tyr223 is found for all complexes studied. However, while the active site group Tyr238-OH interacts with the carboxylate in the case of the substrate D-alanine, of D-CF(3)-alanine, or of L-lactate, in the anthranilate complex the phenol group rotates around the C2-C3 bond thus opening the entrance of the active site, and interacts there with the second bound anthranilate. This movement serves in channeling substrate to the bottom of the active site, the locus of chemical catalysis. The absence in RgDAAO of the "lid" covering the active site, as found in mammalian DAAO, is interpreted as being at the origin of the differences in kinetic mechanism between the two enzymes. This lid has been proposed to regulate product dissociation in the latter, while the side-chain of Tyr238 might exert a similar role in RgDAAO. The more open active site architecture of RgDAAO is the origin of its much broader substrate specificity. The RgDAAO enzyme forms a homodimer with C2 symmetry that is different from that reported for mammalian D-amino acid oxidase. This different mode of aggregation probably causes the differences in stability and tightness of FAD cofactor binding between the DAAOs from different sources.

Yeast D-amino acid oxidase: structural basis of its catalytic properties.,Pollegioni L, Diederichs K, Molla G, Umhau S, Welte W, Ghisla S, Pilone MS J Mol Biol. 2002 Nov 29;324(3):535-46. PMID:12445787^[1]

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

References

↑ Pollegioni L, Diederichs K, Molla G, Umhau S, Welte W, Ghisla S, Pilone MS. Yeast D-amino acid oxidase: structural basis of its catalytic properties. J Mol Biol. 2002 Nov 29;324(3):535-46. PMID:12445787

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/1c0i"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF D-AMINO ACID OXIDASE IN COMPLEX WITH TWO ANTHRANYLATE MOLECULES==
-<StructureSection load='1c0i' size='340' side='right' caption='[[1c0i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1c0i' size='340' side='right'caption='[[1c0i]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1c0i]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_6016 Cbs 6016]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0I OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C0I FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1c0i]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rhodotorula_toruloides Rhodotorula toruloides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C0I FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BE2:2-AMINOBENZOIC+ACID'>BE2</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]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1c0k|1c0k]], [[1c0l|1c0l]], [[1c0p|1c0p]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BE2:2-AMINOBENZOIC+ACID'>BE2</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'>[http://en.wikipedia.org/wiki/D-amino-acid_oxidase D-amino-acid oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.3 1.4.3.3] </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=1c0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0i OCA], [https://pdbe.org/1c0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c0i RCSB], [https://www.ebi.ac.uk/pdbsum/1c0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0i 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=1c0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c0i OCA], [http://pdbe.org/1c0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c0i RCSB], [http://www.ebi.ac.uk/pdbsum/1c0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1c0i ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO]] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
+[https://www.uniprot.org/uniprot/OXDA_RHOTO OXDA_RHOTO] This enzyme can effectively convert cephalosporin C into 7-beta-(5-carboxy-5-oxopentanamido)-cephalosporinic acid.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/1c0i_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c0/1c0i_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 29: @@
 </div>
 <div class="pdbe-citations 1c0i" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Amino acid oxidase 3D structures|Amino acid oxidase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Cbs 6016]]
+[[Category: Large Structures]]
-[[Category: D-amino-acid oxidase]]
+[[Category: Rhodotorula toruloides]]
-[[Category: Diederichs, K]]
+[[Category: Diederichs K]]
-[[Category: Ghisla, S]]
+[[Category: Ghisla S]]
-[[Category: Molla, G]]
+[[Category: Molla G]]
-[[Category: Pilone, M S]]
+[[Category: Pilone MS]]
-[[Category: Pollegioni, L]]
+[[Category: Pollegioni L]]
-[[Category: Umhau, S]]
+[[Category: Umhau S]]
-[[Category: Welte, W]]
+[[Category: Welte W]]
-[[Category: Alpha-beta-alpha motif]]
-[[Category: Flavin containing protein]]
-[[Category: Oxidoreductase]]

1c0i

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF D-AMINO ACID OXIDASE IN COMPLEX WITH TWO ANTHRANYLATE MOLECULES

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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