1EVI - JenaLib

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Title :   THREE-DIMENSIONAL STRUCTURE OF THE PURPLE INTERMEDIATE OF PORCINE KIDNEY D-AMINO ACID OXIDASE

Authors :   H. Mizutani, I. Miyahara, K. Hirotsu, Y. Nishina, K. Shiga, C. Setoyama, R. Miura

Date :   20 Apr 00 (Deposition) - 23 Oct 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Flavoenzyme, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Mizutani, I. Miyahara, K. Hirotsu, Y. Nishina, K. Shiga, C. Setoyama, R. Miura
Three-Dimensional Structure Of The Purple Intermediate Of Porcine Kidney D-Amino Acid Oxidase. Optimization Of The Oxidative Half-Reaction Through Alignment Of The Product With Reduced Flavin.
J. Biochem. (Tokyo) V. 128 73 2000
PubMed-ID: 10876160
(for further references see the PDB file header)

Molecule 1 - D-AMINO ACID OXIDASE
	Chains	:	A, B
	EC Number	:	1.4.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11D
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organ	:	KIDNEY
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	2PC	2	Ligand/Ion	3,4-DIHYDRO-2H-PYRROLIUM-5-CARBOXYLATE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:7 , ALA A:8 , GLY A:9 , ILE A:11 , ALA A:36 , ASP A:37 , ARG A:38 , THR A:43 , THR A:44 , THR A:45 , ALA A:48 , ALA A:49 , GLY A:50 , LEU A:51 , ARG A:162 , LYS A:163 , VAL A:164 , THR A:182 , GLY A:183 , TRP A:185 , LEU A:189 , ILE A:202 , ARG A:283 , GLY A:312 , GLY A:313 , TYR A:314 , GLY A:315 , LEU A:316 , THR A:317 , 2PC A:352 , HOH A:508 , HOH A:603 , HOH A:620 , HOH A:629	BINDING SITE FOR RESIDUE FAD A 351
2	AC2	SOFTWARE	GLN A:53 , TYR A:224 , TYR A:228 , ARG A:283 , GLY A:313 , FAD A:351	BINDING SITE FOR RESIDUE 2PC A 352
3	AC3	SOFTWARE	GLY B:7 , ALA B:8 , GLY B:9 , ILE B:11 , ALA B:36 , ASP B:37 , ARG B:38 , THR B:43 , THR B:44 , THR B:45 , ALA B:48 , ALA B:49 , GLY B:50 , LEU B:51 , ARG B:162 , LYS B:163 , VAL B:164 , THR B:182 , GLY B:183 , TRP B:185 , ILE B:202 , GLY B:281 , ARG B:283 , GLY B:312 , GLY B:313 , TYR B:314 , GLY B:315 , LEU B:316 , THR B:317 , 2PC B:354 , HOH B:402 , HOH B:405 , HOH B:421 , HOH B:515 , HOH B:658	BINDING SITE FOR RESIDUE FAD B 353
4	AC4	SOFTWARE	TYR B:224 , TYR B:228 , ARG B:283 , GLY B:313 , FAD B:353	BINDING SITE FOR RESIDUE 2PC B 354

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

Asymmetric/Biological Unit

No.	Residues
1	Thr A:40	-	Pro A:41
2	Thr B:40	-	Pro B:41

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DAO	PS00677	D-amino acid oxidases signature.	OXDA_PIG	305-323	2	A:305-323 B:305-323

(no "Exon" information available for 1EVI)

Asymmetric/Biological 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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:340
 aligned with OXDA_PIG | P00371 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
             OXDA_PIG     1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPYIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFRPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLL 340
               SCOP domains d1evia1 A:1-194,A:288-340 D-aminoacid oxidase, N-terminal domain                                                                                                                                  d1evia2 A:195-287 D-aminoacid oxidase                                                        d1evia1 A:1-194,A:288-340                             SCOP domains
               CATH domains 1eviA01 A:1-88,A:140-195,A:286-339 NAD(P)-binding Rossmann-like Domain                  1eviA02 A:89-139,A:196-285                         1eviA01 A:1-88,A:140-195,A:286-339                      1eviA02 A:89-139,A:196-285 D-Amino Acid Oxidase, subunit A, domain 2                      1eviA01 A:1-88,A:140-195,A:286-339                    - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh......eeeeee......hhhhhh.............hhhhhhhhhhhhhhhh.....hhhhh.eeeeeeeeee.............eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhhh.eeee....hhhhhhh....eeee.hhhhh.........eeeeeeeeeee......eeee...........eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee....eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DAO  PDB: A:305-323----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1evi A   1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPYIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFRPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLL 340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

Chain B from PDB  Type:PROTEIN  Length:340
 aligned with OXDA_PIG | P00371 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
             OXDA_PIG     1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPYIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFRPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLL 340
               SCOP domains d1evib1 B:1-194,B:288-340 D-aminoacid oxidase, N-terminal domain                                                                                                                                  d1evib2 B:195-287 D-aminoacid oxidase                                                        d1evib1 B:1-194,B:288-340                             SCOP domains
               CATH domains 1eviB01 B:1-88,B:140-195,B:286-339 NAD(P)-binding Rossmann-like Domain                  1eviB02 B:89-139,B:196-285                         1eviB01 B:1-88,B:140-195,B:286-339                      1eviB02 B:89-139,B:196-285 D-Amino Acid Oxidase, subunit A, domain 2                      1eviB01 B:1-88,B:140-195,B:286-339                    - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhh......eeeeee......hhhhhh............hhhhhhhhhhhhhhhhh......hhhh.eeeeeeeeee......hhhhhh.eeeee.hhhhhh......eeeeeeeeeehhhhhhhhhhhhhhhh..eeee....hhhhhhhhh..eeee.hhhhhhhh......eeeeeeeeeee......eeeee..........eeee....eeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee....eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DAO  PDB: B:305-323----------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1evi B   1 MRVVVIGAGVIGLSTALCIHERYHSVLQPLDVKVYADRFTPFTTTDVAAGLWQPYTSEPSNPQEANWNQQTFNYLLSHIGSPNAANMGLTPVSGYNLFREAVPDPYWKDMVLGFRKLTPRELDMFPDYRYGWFNTSLILEGRKYLQWLTERLTERGVKFFLRKVESFEEVARGGADVIINCTGVWAGVLQPDPLLQPGRGQIIKVDAPWLKNFIITHDLERGIYNSPYIIPGLQAVTLGGTFQVGNWNEINNIQDHNTIWEGCCRLEPTLKDAKIVGEYTGFRPVRPQVRLEREQLRFGSSNTEVIHNYGHGGYGLTIHWGCALEVAKLFGKVLEERNLL 340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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)

Pig (Sus scrofa) (6)

1a	1eviA02	A:89-139,A:196-285
1b	1eviB02	B:89-139,B:196-285

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

Topology: Rossmann fold (7312)

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

Pig (Sus scrofa) (21)

2a	1eviA01	A:1-88,A:140-195,A:286-339
2b	1eviB01	B:1-88,B:140-195,B:286-339

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (OXDA_PIG | P00371)

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:0048037	cofactor binding	Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
	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.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0055130	D-alanine catabolic process	The chemical reactions and pathways resulting in the breakdown of D-alanine, the D-enantiomer of the amino acid alanine.
	GO:0046416	D-amino acid metabolic process	The chemical reactions and pathways involving D-amino acids, the D-enantiomers of amino acids.
	GO:0036088	D-serine catabolic process	The chemical reactions and pathways resulting in the breakdown of D-serine, the D-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
	GO:0070178	D-serine metabolic process	The chemical reactions and pathways involving D-serine, the D-enantiomer of serine, i.e. (2R)-2-amino-3-hydroxypropanoic acid.
	GO:0042416	dopamine biosynthetic process	The chemical reactions and pathways resulting in the formation of dopamine, a catecholamine neurotransmitter and a metabolic precursor of noradrenaline and adrenaline.
	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.
	GO:0006562	proline catabolic process	The chemical reactions and pathways resulting in the breakdown of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005741	mitochondrial outer membrane	The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
	GO:0005778	peroxisomal membrane	The lipid bilayer surrounding a peroxisome.
	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/Biological Unit
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		Thr B:40 - Pro B:41	[ RasMol ]

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	OXDA_PIG \| P00371	:	1an9 1dao 1ddo 1kif 1ve9 3wgt 4yjd 4yjf 4yjg 4yjh

1aa8	1AA8 CONTAINS THE SAME PROTEIN COMPLEXED WITH BENZOATE
1an9	1AN9 CONTAINS THE SAME PROTEIN COMPLEXED WITH 2- AMINOBENZOATE

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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