1XXJ - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   URATE OXIDASE FROM ASPERGILLUS FLAVUS COMPLEXED WITH 5-AMINO 6-NITRO URACIL

Authors :   P. Retailleau, N. Colloc'H, D. Vivares, F. Bonnete, B. Castro, M. El Hajji, T. Prange

Date :   05 Nov 04 (Deposition) - 22 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Oxidoreductase, Uric Acid Degradation, Dimeric Barrel, Tunnel-Shaped Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Retailleau, N. Colloc'H, D. Vivares, F. Bonnete, B. Castro, M. El Hajji, T. Prange
Urate Oxidase From Aspergillus Flavus: New Crystal-Packing Contacts In Relation To The Content Of The Active Site.
Acta Crystallogr. , Sect. D V. 61 218 2005
PubMed-ID: 15735331 | Reference-DOI: 10.1107/S0907444904031531
(for further references see the PDB file header)

Molecule 1 - URICASE
	Chains	:	A, B, C, D
	EC Number	:	1.7.3.3
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Taxid	:	4932
	Organism Scientific	:	ASPERGILLUS FLAVUS
	Organism Taxid	:	5059
	Synonym	:	URATE OXIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 9)

No.	Name	Count	Type	Full Name
1	BNZ	1	Ligand/Ion	BENZENE
2	SAC	4	Mod. Amino Acid	N-ACETYL-SERINE
3	UNC	4	Ligand/Ion	5-AMINO-6-NITROPYRIMIDINE-2,4(1H,3H)-DIONE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:159 , ARG A:176 , VAL A:227 , GLN A:228 , ASN A:254 , ILE B:54 , ALA B:56 , THR B:57 , ASP B:58 , HOH B:1001	BINDING SITE FOR RESIDUE UNC A 999
2	AC2	SOFTWARE	ALA A:56 , THR A:57 , HOH A:1008 , PHE B:159 , ARG B:176 , SER B:226 , VAL B:227 , GLN B:228 , ASN B:254	BINDING SITE FOR RESIDUE UNC B 1999
3	AC3	SOFTWARE	PHE C:159 , ARG C:176 , VAL C:227 , GLN C:228 , ASN C:254 , ALA D:56 , THR D:57 , ASP D:58	BINDING SITE FOR RESIDUE UNC C 2999
4	AC4	SOFTWARE	ILE C:54 , ALA C:56 , THR C:57 , ASP C:58 , PHE D:159 , LEU D:170 , ARG D:176 , SER D:226 , VAL D:227 , GLN D:228	BINDING SITE FOR RESIDUE UNC D 3999
5	AC5	SOFTWARE	TRP C:174	BINDING SITE FOR RESIDUE BNZ C 931

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

Asymmetric/Biological Unit

No.	Residues
1	Thr A:74	-	Pro A:75
2	Asp A:283	-	Pro A:284
3	Thr B:74	-	Pro B:75
4	Asp B:283	-	Pro B:284
5	Thr C:74	-	Pro C:75
6	Asp C:283	-	Pro C:284
7	Thr D:74	-	Pro D:75
8	Asp D:283	-	Pro D:284

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

Asymmetric/Biological Unit (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 B:149-176 C:149-176 D:149-176

(no "Exon" information available for 1XXJ)

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:295
 aligned with URIC_ASPFL | Q00511 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
           URIC_ASPFL     2 SAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 296
               SCOP domains d1xxja1 A:1-136 Urate oxidase (uricase)                                                                                                 d1xxja2 A:137-295 Urate oxidase (uricase)                                                                                                                       SCOP domains
               CATH domains -1xxjA00 A:2-295 Urate Oxidase;                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeee.hhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeee..eeeeeeee.....eeeeeeeee....eeeeeeeeeeeeee........................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee..eee...........hhhhh.eeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: A:149-176     ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxj A   1 sAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 295
                            |       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     
                            |                                                                                                                                                                                                                                                                                                      
                            1-SAC

Chain B from PDB  Type:PROTEIN  Length:295
 aligned with URIC_ASPFL | Q00511 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
           URIC_ASPFL     2 SAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 296
               SCOP domains d1xxjb1 B:1-136 Urate oxidase (uricase)                                                                                                 d1xxjb2 B:137-295 Urate oxidase (uricase)                                                                                                                       SCOP domains
               CATH domains -1xxjB00 B:2-295 Urate Oxidase;                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeee..hhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeee..eeeeeeee.....eeeeeeeee...eeeeeeeeeeeeeee........................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee..eee...........hhhhh.eeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: B:149-176     ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxj B   1 sAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 295
                            |       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     
                            1-SAC

Chain C from PDB  Type:PROTEIN  Length:295
 aligned with URIC_ASPFL | Q00511 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
           URIC_ASPFL     2 SAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 296
               SCOP domains d1xxjc1 C:1-136 Urate oxidase (uricase)                                                                                                 d1xxjc2 C:137-295 Urate oxidase (uricase)                                                                                                                       SCOP domains
               CATH domains -1xxjC00 C:2-295 Urate Oxidase;                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeee.hhhhhh..hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeee..eeeeeeee.....eeeeeeeee...eeeeeeeeeeeeeee........................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee..eee...........hhhhh.eeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: C:149-176     ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxj C   1 sAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 295
                            |       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     
                            1-SAC

Chain D from PDB  Type:PROTEIN  Length:295
 aligned with URIC_ASPFL | Q00511 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:295
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291     
           URIC_ASPFL     2 SAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 296
               SCOP domains d1xxjd1 D:1-136 Urate oxidase (uricase)                                                                                                 d1xxjd2 D:137-295 Urate oxidase (uricase)                                                                                                                       SCOP domains
               CATH domains -1xxjD00 D:2-295 Urate Oxidase;                                                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------Uricase-1xxjD01 D:141-290                                                                                                                             ----- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------Uricase-1xxjD02 D:141-290                                                                                                                             ----- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------Uricase-1xxjD03 D:141-290                                                                                                                             ----- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------Uricase-1xxjD04 D:141-290                                                                                                                             ----- Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------------------------------------------------------------------------------Uricase-1xxjD05 D:141-290                                                                                                                             ----- Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------------------------------------------------------------------------------Uricase-1xxjD06 D:141-290                                                                                                                             ----- Pfam domains (6)
           Pfam domains (7) --------------------------------------------------------------------------------------------------------------------------------------------Uricase-1xxjD07 D:141-290                                                                                                                             ----- Pfam domains (7)
           Pfam domains (8) --------------------------------------------------------------------------------------------------------------------------------------------Uricase-1xxjD08 D:141-290                                                                                                                             ----- Pfam domains (8)
         Sec.struct. author ..eeeeeeeeeeeeeeeeee......eeeeeeeeeeeeee.hhhhhhh.hhhhh.hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeee..eeeeeeee.....eeeeeeeee....eeeeeeeeeeeeee........................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee..eee...........hhhhh.eeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: D:149-176     ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xxj D   1 sAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRS 295
                            |       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     
                            1-SAC

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)

Aspergillus flavus [TaxId: 5059] (53)

1a	d1xxja1	A:1-136
1b	d1xxja2	A:137-295
1c	d1xxjb1	B:1-136
1d	d1xxjb2	B:137-295
1e	d1xxjc1	C:1-136
1f	d1xxjc2	C:137-295
1g	d1xxjd1	D:1-136
1h	d1xxjd2	D:137-295

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)

Aspergillus flavus. Organism_taxid: 5059. (14)

1a	1xxjA00	A:2-295
1b	1xxjB00	B:2-295
1c	1xxjC00	C:2-295
1d	1xxjD00	D:2-295

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: THBO-biosyn (64)

Family: Uricase (35)

Aspergillus flavus (35)

1a	Uricase-1xxjD01	D:141-290
1b	Uricase-1xxjD02	D:141-290
1c	Uricase-1xxjD03	D:141-290
1d	Uricase-1xxjD04	D:141-290
1e	Uricase-1xxjD05	D:141-290
1f	Uricase-1xxjD06	D:141-290
1g	Uricase-1xxjD07	D:141-290
1h	Uricase-1xxjD08	D:141-290

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:283 - Pro A:284	[ RasMol ]
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	1xxj
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1wrr	THE SAME COMPLEX BUT IN ANOTHER SPACEGROUP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 8)

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