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Title :   CRYSTAL STRUCTURE OF URATE OXIDASE FROM BACILLUS SP. TB-90 CO-CRYSTALLIZED WITH 8-AZAXANTHINE

Authors :   T. Hibi, T. Nago, Y. Nishiya, J. Oda

Date :   05 Jan 03 (Deposition) - 15 Jun 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   T-Fold Barrel, Purine, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Hibi, T. Nago, Y. Nishiya, J. Oda
Crystal Structure Of Urate Oxidase From Bacillus Sp.
To Be Published
PubMed: search

Molecule 1 - URICASE
	Chains	:	A, B, C, D
	EC Number	:	1.7.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUO6
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-319
	Organism Scientific	:	BACILLUS SP.
	Organism Taxid	:	36824
	Strain	:	TB-90
	Synonym	:	URATE OXIDASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	AZA	4	Ligand/Ion	8-AZAXANTHINE
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:298 , ARG D:298	BINDING SITE FOR RESIDUE SO4 B 501
2	AC2	SOFTWARE	LYS A:106 , ASP A:190 , GLU A:191 , HOH A:4349 , LYS B:106	BINDING SITE FOR RESIDUE SO4 A 502
3	AC3	SOFTWARE	THR A:31 , ARG D:133	BINDING SITE FOR RESIDUE SO4 D 503
4	AC4	SOFTWARE	ARG A:298 , ARG C:298	BINDING SITE FOR RESIDUE SO4 A 504
5	AC5	SOFTWARE	PHE A:184 , LEU A:195 , ARG A:201 , SER A:248 , ILE A:249 , GLN A:250 , ASN A:276 , HOH A:4388 , TYR B:11 , ALA B:72 , THR B:73	BINDING SITE FOR RESIDUE AZA A 4320
6	AC6	SOFTWARE	TYR A:11 , ALA A:72 , THR A:73 , PHE B:184 , LEU B:195 , ARG B:201 , SER B:248 , ILE B:249 , GLN B:250 , ASN B:276 , HOH B:1363	BINDING SITE FOR RESIDUE AZA B 1320
7	AC7	SOFTWARE	PHE C:184 , ARG C:201 , SER C:248 , ILE C:249 , GLN C:250 , ASN C:276 , HOH C:2419 , TYR D:11 , ALA D:72 , THR D:73	BINDING SITE FOR RESIDUE AZA C 2320
8	AC8	SOFTWARE	THR C:73 , PHE D:184 , LEU D:195 , ARG D:201 , SER D:248 , ILE D:249 , GLN D:250 , ASN D:276	BINDING SITE FOR RESIDUE AZA D 3320

(no "SS Bond" information available for 1J2G)

(no "Cis Peptide Bond" information available for 1J2G)

(no "SAP(SNP)/Variant" information available for 1J2G)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	URICASE	PS00366	Uricase signature.	PUCL_BACSB	344-371	4	A:174-201 B:174-201 C:174-201 D:174-201

(no "Exon" information available for 1J2G)

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:306
 aligned with PUCL_BACSB | Q45697 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:306
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476      
           PUCL_BACSB   177 RVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQED 482
               SCOP domains d1j2ga1 A:7-158 Urate oxidase (uricase)                                                                                                                 d1j2ga2 A:159-312 Urate oxidase (uricase)                                                                                                                  SCOP domains
               CATH domains 1j2gA00 A:7-312 Urate Oxidase;                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......................eeeeeeeeeee...hhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeeeeeeee.eeeeeeee..eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeeeeeeeeee........................eeeeeeeeeee.hhhhhhh.hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee...eeee.........eee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: A:174-201     --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j2g A   7 RVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQED 312
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

Chain B from PDB  Type:PROTEIN  Length:306
 aligned with PUCL_BACSB | Q45697 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:306
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476      
           PUCL_BACSB   177 RVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQED 482
               SCOP domains d1j2gb1 B:7-158 Urate oxidase (uricase)                                                                                                                 d1j2gb2 B:159-312 Urate oxidase (uricase)                                                                                                                  SCOP domains
               CATH domains 1j2gB00 B:7-312 Urate Oxidase;                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......................eeeeeeeeeeehhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee..eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeeeeeeeeee.........................eeeeeeeeee.hhhhhh..hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee...eeee.........eee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: B:174-201     --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j2g B   7 RVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQED 312
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

Chain C from PDB  Type:PROTEIN  Length:306
 aligned with PUCL_BACSB | Q45697 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:306
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476      
           PUCL_BACSB   177 RVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQED 482
               SCOP domains d1j2gc1 C:7-158 Urate oxidase (uricase)                                                                                                                 d1j2gc2 C:159-312 Urate oxidase (uricase)                                                                                                                  SCOP domains
               CATH domains 1j2gC00 C:7-312 Urate Oxidase;                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......................eeeeeeeeeeehhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee..eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeeeeeeeeee........................eeeeeeeeeee.hhhhhhh.hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee...eeee.........eee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: C:174-201     --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j2g C   7 RVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQED 312
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

Chain D from PDB  Type:PROTEIN  Length:306
 aligned with PUCL_BACSB | Q45697 from UniProtKB/Swiss-Prot  Length:502

    Alignment length:306
                                   186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476      
           PUCL_BACSB   177 RVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQED 482
               SCOP domains d1j2gd1 D:7-158 Urate oxidase (uricase)                                                                                                                 d1j2gd2 D:159-312 Urate oxidase (uricase)                                                                                                                  SCOP domains
               CATH domains 1j2gD00 D:7-312 Urate Oxidase;                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......................eeeeeeeeeee...hhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeeeeeee..eeeeeeee..eeeeeeeeeee....eeeeeeeeee.....eeeeeeeeeeeeeeeee.........................eeeeeeeeee.hhhhhh........hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee...eeee.........eee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: D:174-201     --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j2g D   7 RVMYYGKGDVFAYRTYLKPLTGVRTIPESPFSGRDHILFGVNVKISVGGTKLLTSFTKGDNSLVVATDSMKNFIQKHLASYTGTTIEGFLEYVATSFLKKYSHIEKISLIGEEIPFETTFAVKNGNRAASELVFKKSRNEYATAYLNMVRNEDNTLNITEQQSGLAGLQLIKVSGNSFVGFIRDEYTTLPEDSNRPLFVYLNIKWKYKNTEDSFGTNPENYVAAEQIRDIATSVFHETETLSIQHLIYLIGRRILERFPQLQEVYFESQNHTWDKIVEEIPESEGKVYTEPRPPYGFQCFTVTQED 312
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: T-fold (116)

Superfamily: Tetrahydrobiopterin biosynthesis enzymes-like (113)

Family: Urate oxidase (uricase) (60)

Protein domain: Urate oxidase (uricase) (56)

Bacillus sp., strain TB-90 [TaxId: 1409] (1)

1a	d1j2ga1	A:7-158
1b	d1j2ga2	A:159-312
1c	d1j2gb1	B:7-158
1d	d1j2gb2	B:159-312
1e	d1j2gc1	C:7-158
1f	d1j2gc2	C:159-312
1g	d1j2gd1	D:7-158
1h	d1j2gd2	D:159-312

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Urate Oxidase (38)

Homologous Superfamily: Urate Oxidase; (38)

Bacillus sp.. Organism_taxid: 36824. Strain: tb-90. (1)

1a	1j2gA00	A:7-312
1b	1j2gB00	B:7-312
1c	1j2gC00	C:7-312
1d	1j2gD00	D:7-312

(no "Pfam Domain" information available for 1J2G)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (PUCL_BACSB | Q45697)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	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:0004846	urate oxidase activity	Catalysis of the reaction: urate + O2 + H2O = 5-hydroxyisourate + hydrogen peroxide.
biological process
	GO:0019428	allantoin biosynthetic process	The chemical reactions and pathways resulting in the formation of allantoin, (2,5-dioxo-4-imidazolidinyl)urea.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0006144	purine nucleobase metabolic process	The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
	GO:0019628	urate catabolic process	The chemical reactions and pathways resulting in the breakdown of urate, the anion of uric acid, 2,6,8-trioxypurine.

Asymmetric/Biological Unit
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1uox	URATE OXIDASE FROM ASPERGILLUS FLAVUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

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SCOP Domains (1, 8)

CATH Domains (1, 4)

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