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(-) Description

Title :  CRYSTAL STRUCTURE OF COFACTOR-FREE URATE OXIDASE IN COMPLEX WITH THE 5-PEROXO DERIVATIVE OF 9-METYL URIC ACID (X-RAY DOSE, 2.5 KGY)
 
Authors :  S. Bui, R. A. Steiner
Date :  01 Apr 14  (Deposition) - 29 Oct 14  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Oxidoreductase, Cofactor-Free Oxidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bui, D. Von Stetten, P. G. Jambrina, T. Prang, N. Colloc'H, D. De Sanctis, A. Royant, E. Rosta, R. A. Steiner
Direct Evidence For A Peroxide Intermediate And A Reactive Enzyme-Substrate-Dioxygen Configuration In A Cofactor-Free Oxidase.
Angew. Chem. Int. Ed. Engl. V. 53 13710 2014
PubMed-ID: 25314114  |  Reference-DOI: 10.1002/ANIE.201405485

(-) Compounds

Molecule 1 - URICASE
    Chains: A
    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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SAC1Mod. Amino AcidN-ACETYL-SERINE
3XDS1Ligand/Ion(5S)-5-(DIOXIDANYL)-9-METHYL-7H-PURINE-2,6,8-TRIONE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2SAC4Mod. Amino AcidN-ACETYL-SERINE
3XDS4Ligand/Ion(5S)-5-(DIOXIDANYL)-9-METHYL-7H-PURINE-2,6,8-TRIONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:54 , ALA A:56 , THR A:57 , ASP A:58 , PHE A:159 , LEU A:170 , ARG A:176 , SER A:226 , VAL A:227 , GLN A:228 , ASN A:254 , HIS A:256 , GLY A:286 , ILE A:288BINDING SITE FOR RESIDUE XDS A 1303
2AC2SOFTWAREGLN A:158 , TRP A:174 , SER A:192 , HOH A:2386 , HOH A:2469BINDING SITE FOR RESIDUE MPD A 1304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CW2)

(-) Cis Peptide Bonds  (2, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CW2)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1URICASEPS00366 Uricase signature.URIC_ASPFL150-177  1A:149-176
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1URICASEPS00366 Uricase signature.URIC_ASPFL150-177  4A:149-176

(-) Exons   (0, 0)

(no "Exon" information available for 4CW2)

(-) Sequences/Alignments

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
(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:301
 aligned with URIC_ASPFL | Q00511 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:301
                                    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       301 
           URIC_ASPFL     2 SAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRSSLKSKL 302
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeeee......eeeeeeeeeeeeee.hhhhhhh.hhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeee..eeeeeeee.....eeeeeeeee....eeeeeeeeeeeeee........................eeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeeeeeeeee..eee...........hhhhh..eee.....eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------URICASE  PDB: A:149-176     ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cw2 A   1 sAVKAARYGKDNVRVYKVHKDEKTGVQTVYEMTVCVLLEGEIETSYTKADNSVIVATDSIKNTIYITAKQNPVTPPELFGSILGTHFIEKYNHIHAAHVNIVCHRWTRMDIDGKPHPHSFIRDSEEKRNVQVDVVEGKGIDIKSSLSGLTVLKSTNSQFWGFLRDEYTTLKETWDRILSTDVDATWQWKNFSGLQEVRSHVPKFDATWATAREVTLKTFAEDNSASVQATMYKMAEQILARQQLIETVEYSLPNKHYFEIDLSWHKGLQNTGKNAEVFAPQSDPNGLIKCTVGRSSLKSKL 301
                            |       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 
                            |                                                                                                                                                                                                                                                                                                            
                            1-SAC
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4CW2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CW2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CW2)

(-) Gene Ontology  (6, 6)

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        URIC_ASPFL | Q00511: 1r4s 1r4u 1r51 1r56 1wrr 1ws2 1ws3 1xt4 1xxj 1xy3 2fub 2fxl 2iba 2ic0 2icq 2pes 2zka 2zkb 3bjp 3bk8 3cks 3cku 3f2m 3gko 3l8w 3l9g 3lbg 3ld4 3obp 3p9f 3p9o 3pjk 3pk3 3pk4 3pk5 3pk6 3pk8 3pkf 3pkg 3pkh 3pkk 3pkl 3pks 3pkt 3pku 3ple 3plg 3plh 3pli 3plj 3plm 4cw0 4cw3 4cw6 4d12 4d13 4d17 4d19 4fsk 4n3m 4n9m 4n9s 4n9v 4op6 4op9 4oqc 4poe 4pr8 4puv 5frc

(-) Related Entries Specified in the PDB File

4cw0 CRYSTAL STRUCTURE OF COFACTOR-FREE URATE OXIDASE ANAEROBICALLY COMPLEXED WITH 9-METHYL URIC ACID
4cw3 CRYSTAL STRUCTURE OF COFACTOR-FREE URATE OXIDASE IN COMPLEX WITH THE 5-PEROXO DERIVATIVE OF 9-METYL URIC ACID (X-RAY DOSE, 665 KGY)
4cw6 CRYSTAL STRUCTURE OF COFACTOR-FREE URATE OXIDASE IN COMPLEX WITH THE 5-PEROXO DERIVATIVE OF 9-METYL URIC ACID (X-RAY DOSE, 92 KGY)