1C0I - JenaLib

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

Authors :   L. Pollegioni, K. Diederichs, G. Molla, S. Umhau, W. Welte, S. Ghisla, M. S. Pilone

Date :   16 Jul 99 (Deposition) - 27 Feb 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Flavin Containing Protein, Alpha-Beta-Alpha Motif, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Pollegioni, K. Diederichs, G. Molla, S. Umhau, W. Welte, S. Ghisla, M. S. Pilone
Yeast D-Amino Acid Oxidase: Structural Basis Of Its Catalytic Properties
J. Mol. Biol. V. 324 535 2002
PubMed-ID: 12445787 | Reference-DOI: 10.1016/S0022-2836(02)01062-8
(for further references see the PDB file header)

Molecule 1 - D-AMINO ACID OXIDASE
	Chains	:	A
	EC Number	:	1.4.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7.7
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	RHODOSPORIDIUM TORULOIDES
	Organism Taxid	:	5286

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	BE2	2	Ligand/Ion	2-AMINOBENZOIC ACID
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	BE2	4	Ligand/Ion	2-AMINOBENZOIC ACID
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:1011 , SER A:1012 , GLY A:1013 , VAL A:1014 , ILE A:1015 , ALA A:1034 , ARG A:1035 , ASP A:1036 , PHE A:1046 , ALA A:1047 , SER A:1048 , TRP A:1050 , ALA A:1051 , GLY A:1052 , ALA A:1053 , ASN A:1054 , ARG A:1160 , THR A:1161 , VAL A:1162 , ALA A:1178 , THR A:1179 , GLY A:1182 , ILE A:1186 , THR A:1201 , TYR A:1223 , ARG A:1285 , SER A:1334 , SER A:1335 , ALA A:1336 , GLY A:1337 , TYR A:1338 , GLN A:1339 , BE2 A:1364 , HOH A:2001 , HOH A:2002 , HOH A:2009 , HOH A:2035 , HOH A:2039	BINDING SITE FOR RESIDUE FAD A 1363
2	AC2	SOFTWARE	ASN A:1054 , PHE A:1058 , TYR A:1223 , ILE A:1225 , ARG A:1285 , SER A:1335 , FAD A:1363 , BE2 A:1365	BINDING SITE FOR RESIDUE BE2 A 1364
3	AC3	SOFTWARE	PHE A:1058 , TYR A:1238 , BE2 A:1364	BINDING SITE FOR RESIDUE BE2 A 1365

(no "SS Bond" information available for 1C0I)

Asymmetric Unit

No.	Residues
1	Gly A:1052	-	Ala A:1053
2	Leu A:1301	-	Pro A:1302

(no "SAP(SNP)/Variant" information available for 1C0I)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAO	PS00677	D-amino acid oxidases signature.	OXDA_RHOTO	327-345	1	A:1327-1345

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAO	PS00677	D-amino acid oxidases signature.	OXDA_RHOTO	327-345	2	A:1327-1345

(no "Exon" information available for 1C0I)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:363
 aligned with OXDA_RHOTO | P80324 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:363
                              1                                                                                                                                                                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   
          OXDA_RHOTO      - --MHSQKRVVVLGSGVIGLSSALILARKGYSVHILARDLPEDVSSQTFASPWAGANWTPFMTLTDGPRQAKWEESTFKKWVELVPTGHAMWLKGTRRFAQNEDGLLGHWYKDITPNYRPLPSSECPPGAIGVTYDTLSVHAPKYCQYLARELQKLGATFERRTVTSLEQAFDGADLVVNATGLGAKSIAGIDDQAAEPIRGQTVLVKSPCKRCTMDSSDPASPAYIIPRPGGEVICGGTYGVGDWDLSVNPETVQRILKHCLRLDPTISSDGTIEGIEVLRHNVGLRPARRGGPRVEAERIVLPLDRTKSPLSLGRGSARAAKEKEVTLVHAYGFSSAGYQQSWGAAEDVAQLVDEAFQRYHG  361
               SCOP domains d1c0ia1 A:999-1193,A:1289-1361 D-aminoacid oxidase, N-terminal domain                                                                                                                              d1c0ia2 A:1194-1288 D-aminoacid oxidase                                                        d1c0ia1 A:999-1193,A:1289-1361 D-aminoacid oxidase, N-terminal domain     SCOP domains
               CATH domains 1c0iA01 A:999-1076,A:1138-1185,A:1289-1361 NAD(P)-binding Rossmann-like Domain1c0iA02 A:1077-1136,A:1186-1288                             -1c0iA01 A:999-1076,A:1138-1185,A:1289-1361      1c0iA02 A:1077-1136,A:1186-1288 D-Amino Acid Oxidase, subunit A, domain 2                              1c0iA01 A:999-1076,A:1138-1185,A:1289-1361                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee..hhhhhhhhhhhhhh..eeeeee............hhhhh............hhhhhhhhhhhhhhhhhhh.....eeeeeeeeee.hhhhhhhhh........ee.hhhhh....eeeeeeeee.hhhhhhhhhhhhhhhh..eeee.....hhhh.....eeee.hhhhhhh........eeeeeeeeeeee......eee.......eeeeee...eeeee...ee.......hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeeeeeeeee....eeeeeeeee.....................eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DAO                ---------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1c0i A  999 LMMHSQKRVVVLGSGVIGLSSALILARKGYSVHILARDLPEDVSSQTFASPWAGANWTPFMTLTDGPRQAKWEESTFKKWVELVPTGHAMWLKGTRRFAQNEDGLLGHWYKDITPNYRPLPSSECPPGAIGVTYDTLSVHAPKYCQYLARELQKLGATFERRTVTSLEQAFDGADLVVNATGLGAKSIAGIDDQAAEPIRGQTVLVKSPCKRCTMDSSDPASPAYIIPRPGGEVICGGTYGVGDWDLSVNPETVQRILKHCLRLDPTISSDGTIEGIEVLRHNVGLRPARRGGPRVEAERIVLPLDRTKSPLSLGRGSARAAKEKEVTLVHAYGFSSAGYQQSWGAAEDVAQLVDEAFQRYHG 1361
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-Amino Acid Oxidase; Chain A, domain 2 (80)

Homologous Superfamily: D-Amino Acid Oxidase, subunit A, domain 2 (80)

Rhodosporidium toruloides. Organism_taxid: 5286. (4)

1c0iA02

A:1077-1136,A:1186-1288

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Rhodosporidium toruloides. Organism_taxid: 5286. (4)

1c0iA01

A:999-1076,A:1138-1185,A:1289-1361

(no "Pfam Domain" information available for 1C0I)

Asymmetric Unit(hide GO term definitions)

Chain A (OXDA_RHOTO | P80324)

molecular function
	GO:0003884	D-amino-acid oxidase activity	Catalysis of the reaction: a D-amino acid + H2O + O2 = a 2-oxo acid + NH3 + hydrogen peroxide.
	GO:0071949	FAD binding	Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0046416	D-amino acid metabolic process	The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:1052 - Ala A:1053	[ RasMol ]
		Leu A:1301 - Pro A:1302	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	OXDA_RHOTO \| P80324	:	1c0k 1c0l 1c0p 2dzg

1c0k	CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH L-LACTATE
1c0l	CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH TRIFLUOROALANINE
1c0p	CRYSTAL STRUCTURE ANALYSIS OF D-AMINO ACID OXIDASE IN COMPLEX WITH D-ALANINE

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