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(-) Description

Title :  CRYSTAL STRUCTURE OF UROPORPHYRINOGEN III SYNTHASE FROM AN EXTREMELY THERMOPHILIC BACTERIUM THERMUS THERMOPHILUS HB8 (WILD TYPE, NATIVE, FORM-1 CRYSTAL)
 
Authors :  E. Mizohata, T. Matsuura, H. Sakai, K. Murayama, T. Terada, M. Shirouzu S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 May 04  (Deposition) - 06 May 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Uroporphyrinogen, Porphyrin, Congenital Erythropoietic Porphyria, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Mizohata, T. Matsuura, H. Sakai, K. Murayama, T. Terada, M. Shirouzu, S. Kuramitsu, S. Yokoyama
Crystal Structure Of Uroporphyrinogen Iii Synthase From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UROPORPHYRINOGEN III SYNTHASE
    Chains: A
    EC Number: 4.2.1.75
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:97 , GLY A:118 , THR A:119 , SER A:120 , HOH A:1033 , HOH A:1039 , HOH A:1112BINDING SITE FOR RESIDUE GOL A 1001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WCW)

(-) Exons   (0, 0)

(no "Exon" information available for 1WCW)

(-) Sequences/Alignments

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:254
 aligned with Q5SKH2_THET8 | Q5SKH2 from UniProtKB/TrEMBL  Length:253

    Alignment length:254
                             1                                                                                                                                                                                                                                                            
                             |       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    
         Q5SKH2_THET8     - -MRVAYAGLRRKEAFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRALAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEALLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQKEVA 253
               SCOP domains d1wcwa_ A: automated matches                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1wcwA01 A:8-38,A:168-261       -----1wcwA02 A:44-162  [code=3.40.50.10090, no name defined]                                                                -----1wcwA01 A:8-38,A:168-261  [code=3.40.50.10090, no name defined]                                CATH domains
               Pfam domains ------------HEM4-1wcwA01 A:20-250                                                                                                                                                                                                                  ----------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhh..eeee...eeeee.hhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh...hhhhhhhheeee.hhhhhhhhhhh.....ee...hhhhhhhhh....eeeeee.....hhhhhhhhhhh.eeeeee..eeeeehhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh.hhhhhhhhhhhh.eeeeehhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wcw A   8 AVRVAYAGLRRKEAFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRALAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEALLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQKEVA 261
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: HEM4] (6)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5SKH2_THET8 | Q5SKH2)
molecular function
    GO:0004852    uroporphyrinogen-III synthase activity    Catalysis of the reaction: hydroxymethylbilane = H(2)O + uroporphyrinogen III.
biological process
    GO:0033014    tetrapyrrole biosynthetic process    The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

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 Related Entries

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

UniProtKB/TrEMBL
        Q5SKH2_THET8 | Q5SKH2: 1wcx 1wd7

(-) Related Entries Specified in the PDB File

1wcx THE SAME PROTEIN, L75M/I193M/L248M, SEMET DERIVATIVE, FORM- 1 CRYSTAL RELATED ID: TTK003001434.2 RELATED DB: TARGETDB