3P9F - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   URATE OXIDASE-AZAXANTHINE-AZIDE TERNARY COMPLEX

Authors :   L. Gabison, N. Colloc'H, M. El Hajji, B. Castro, M. Chiadmi, T. Prange

Date :   17 Oct 10 (Deposition) - 28 Sep 11 (Release) - 28 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Inhibition, Degradation Mechanism, Peroxisome, Purine Metabolism, Heterotetramer, Oxygen Binding Oxidoreductase, Oxygen Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Gabison, N. Colloc H, M. El Hajji, B. Castro, M. Chiadmi, T. Prange
Azide And Cyanide Have Different Inhibition Modes Of Urate Oxidase
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - URICASE
	Chains	:	A
	EC Number	:	1.7.3.3
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	YEAST
	Expression System Taxid	:	4932
	Gene	:	UAZ, UOX
	Organism Scientific	:	ASPERGILLUS FLAVUS
	Organism Taxid	:	5059
	Synonym	:	URATE OXIDASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	AZA	1	Ligand/Ion	8-AZAXANTHINE
3	AZI	2	Ligand/Ion	AZIDE ION
4	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	ACE	4	Mod. Amino Acid	ACETYL GROUP
2	AZA	4	Ligand/Ion	8-AZAXANTHINE
3	AZI	8	Ligand/Ion	AZIDE ION
4	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:54 , ALA A:56 , THR A:57 , PHE A:159 , ARG A:176 , SER A:226 , VAL A:227 , GLN A:228 , ASN A:254 , AZI A:303 , HOH A:1002	BINDING SITE FOR RESIDUE AZA A 302
2	AC2	SOFTWARE	LYS A:10 , THR A:57 , ASN A:254 , HIS A:256 , GLY A:286 , ILE A:288 , AZA A:302	BINDING SITE FOR RESIDUE AZI A 303
3	AC3	SOFTWARE	ALA A:6 , ARG A:7 , LYS A:289 , HOH A:1319	BINDING SITE FOR RESIDUE AZI A 304
4	AC4	SOFTWARE	ILE A:88 , TYR A:91 , ASN A:92 , ILE A:94 , GLU A:136 , HOH A:1160	BINDING SITE FOR RESIDUE NA A 850

(no "SS Bond" information available for 3P9F)

Asymmetric Unit

No.	Residues
1	Thr A:74	-	Pro A:75
2	Asp A:283	-	Pro A:284

(no "SAP(SNP)/Variant" information available for 3P9F)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	URICASE	PS00366	Uricase signature.	URIC_ASPFL	150-177	1	A:149-176

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	URICASE	PS00366	Uricase signature.	URIC_ASPFL	150-177	4	A:149-176

(no "Exon" information available for 3P9F)

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:296
 aligned with URIC_ASPFL | Q00511 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:296
                                    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      
           URIC_ASPFL     1 MSAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 296
               SCOP domains -d3p9fa1 A:1-136 Urate oxidase (uricase)                                                                                                 d3p9fa2 A:137-295 Urate oxidase (uricase)                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeeeee......eeeeeeeeeeeeee.hhhhhhh.hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeee..eeeeeeee.....eeeeeeeee...eeeeeeeeeeeeeee........................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee..eee...........hhhhh..eee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: A:149-176     ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p9f A   0 xSAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 295
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289      
                            |                                                                                                                                                                                                                                                                                                       
                            0-ACE

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(

)

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)

Aspergillus flavus [TaxId: 5059] (53)

1a	d3p9fa1	A:1-136
1b	d3p9fa2	A:137-295

(no "CATH Domain" information available for 3P9F)

(no "Pfam Domain" information available for 3P9F)

Asymmetric Unit(hide GO term definitions)

Chain A (URIC_ASPFL | Q00511)

molecular function
	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: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.
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.

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	Cis Peptide Bonds
		Asp A:283 - Pro A:284	[ RasMol ]
		Thr A:74 - Pro A:75	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3p9f
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1r4s	URATE OXIDASE FROM ASPERGILLUS FLAVUS COMPLEXED WITH ITS INHIBITOR 9-METHYL URIC ACID
3bjp	URATE OXIDASE CYANIDE URIC ACID TERNARY COMPLEX
3l8w	URATE OXIDASE FROM ASPERGILLUS FLAVUS COMPLEXED WITH XANTHIN
3obp	ANAEROBIC COMPLEX OF URATE OXIDASE WITH URIC ACID
3p9o

Description

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Ligands, Modified Residues, Ions (4, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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