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(-) Description

Title :  CRYSTAL STRUCTURE OF UROPORPHYRINOGEN III SYNTHASE FROM AN EXTREMELY THERMOPHILIC BACTERIUM THERMUS THERMOPHILUS HB8 (WILD TYPE, NATIVE, FORM-2 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 :  12 May 04  (Deposition) - 12 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Uroporphyrinogen, Porphyrin, Heme, 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 An Extremely Thermophilic Bacterium Thermus Thermophilus Hb8 (Wild Type, Native, Form-2 Crystal)
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UROPORPHYRINOGEN III SYNTHASE
    Chains: A, B
    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

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WD7)

(-) Sites  (0, 0)

(no "Site" information available for 1WD7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WD7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WD7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WD7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WD7)

(-) Exons   (0, 0)

(no "Exon" information available for 1WD7)

(-) 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: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 d1wd7a_ A: Probable uroporphyrinogen-III synthase                                                                                                                                                                                                              SCOP domains
               CATH domains 1wd7A01 A:8-43,A:165-261            1wd7A02 A:44-164  [code=3.40.50.10090, no name defined]                                                                  1wd7A01 A:8-43,A:165-261  [code=3.40.50.10090, no name defined]                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhh..eeee........ee..hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh...hhhhhhh.eeee.hhhhhhhhhhh.....ee...hhhhhhhhh....eeeeee.....hhhhhhhhhhh.eeeeee..ee...hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh.hhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wd7 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    


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with Q5SKH2_THET8 | Q5SKH2 from UniProtKB/TrEMBL  Length:253

    Alignment length:255
                              1                                                                                                                                                                                                                                                            
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     
         Q5SKH2_THET8     - --MRVAYAGLRRKEAFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRALAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEALLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQKEVA 253
               SCOP domains d1wd7b_ B: Probable uroporphyrinogen-III synthase                                                                                                                                                                                                               SCOP domains
               CATH domains 1wd7B01 B:7-42,B:165-261            1wd7B02 B:43-164  [code=3.40.50.10090, no name defined]                                                                   1wd7B01 B:7-42,B:165-261  [code=3.40.50.10090, no name defined]                                   CATH domains
           Pfam domains (1) -------------HEM4-1wd7B01 B:20-250                                                                                                                                                                                                                  ----------- Pfam domains (1)
           Pfam domains (2) -------------HEM4-1wd7B02 B:20-250                                                                                                                                                                                                                  ----------- Pfam domains (2)
         Sec.struct. author ...eeee....hhhhhhhhhhhh..eeee........ee..hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh...hhhhhhh.eeee.hhhhhhhhhhh.....ee...hhhhhhhhh....eeeeee.....hhhhhhhhhhh.eeeeee..ee...hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh.hhhhhhhhh....eeeeehhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wd7 B   7 DAVRVAYAGLRRKEAFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRALAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEALLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQKEVA 261
                                    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
   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, 2)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  4.2.1.75
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 Related Entries

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

UniProtKB/TrEMBL
        Q5SKH2_THET8 | Q5SKH2: 1wcw 1wcx

(-) Related Entries Specified in the PDB File

1wcw WILD-TYPE, NATIVE, FORM-1 CRYSTAL
1wcx L75M/I193M/L248M, SEMET DERIVATIVE, FORM-1 CRYSTAL RELATED ID: TTK003001434.1 RELATED DB: TARGETDB