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(-) Description

Title :  THERMUS THERMOPHILUS UROPORPHYRINOGEN III SYNTHASE
 
Authors :  H. L. Schubert
Date :  23 May 08  (Deposition) - 12 Aug 08  (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 :  Heme Biosynthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. L. Schubert, J. D. Phillips, A. Heroux, C. P. Hill
Structure And Mechanistic Implications Of A Uroporphyrinogen Iii Synthase-Product Complex.
Biochemistry V. 47 8648 2008
PubMed-ID: 18651750  |  Reference-DOI: 10.1021/BI800635Y
(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
    Expression System Plasmid: PET151
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: TT_C0312
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 262724
    Strain: HB27

 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  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:89 , THR A:111 , SER A:112 , GLU A:188 , GLU A:223 , HOH A:307 , HOH A:408BINDING SITE FOR RESIDUE ACT A 254
2AC2SOFTWAREGLU A:169 , LEU A:172BINDING SITE FOR RESIDUE ACT A 255
3AC3SOFTWARETHR A:59 , GLY A:60 , VAL A:61 , LYS A:92 , HOH A:341 , HOH A:347 , HOH A:570BINDING SITE FOR RESIDUE ACT A 256
4AC4SOFTWARETHR B:59 , GLY B:60 , VAL B:61 , LYS B:92 , HOH B:311 , HOH B:343 , HOH B:460BINDING SITE FOR RESIDUE ACT B 254

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D8T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D8T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D8T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D8T)

(-) Exons   (0, 0)

(no "Exon" information available for 3D8T)

(-) 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:252
 aligned with Q72KM1_THET2 | Q72KM1 from UniProtKB/TrEMBL  Length:253

    Alignment length:252
                             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  
         Q72KM1_THET2     - -MRIAYAGLRRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQKE 251
               SCOP domains d3d8ta_ A: automated matches                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhhh.eeee...eeeeeee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhh...hhhhhhhheeee.hhhhhhhhhhh.....ee...hhhhhhhhh.....eeeee.....hhhhhhhhhhh..eeeee..eeeeehhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh.hhhhhhhhhh...eeeeehhhhhhhhhhh.....eee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3d8t A  -1 TMRIAYAGLRRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQKE 251
                            ||       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  
                            ||                                                                                                                                                                                                                                                          
                           -1|                                                                                                                                                                                                                                                          
                             1                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with Q72KM1_THET2 | Q72KM1 from UniProtKB/TrEMBL  Length:253

    Alignment length:249
                             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         
         Q72KM1_THET2     - -MRIAYAGLRRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRAL 248
               SCOP domains d3d8tb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhhh..eeee........ee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhh...hhhhhhh.eeee.hhhhhhhhhhh.....ee....hhhhhhhh.....eeeee.....hhhhhhhhhhh..eeeee..ee...hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh.hhhhhhhhhh...eeeeehhhhhhhhhhh.....eee...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d8t B  -1 TMRIAYAGLRRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRAL 248
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239         
                           -1|                                                                                                                                                                                                                                                       
                             1
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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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3D8T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D8T)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q72KM1_THET2 | Q72KM1)
molecular function
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    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
        Q72KM1_THET2 | Q72KM1: 3d8n 3d8r 3d8s

(-) Related Entries Specified in the PDB File

1jr2 STRUCTURE OF UROPORPHYRINOGEN III SYNTHASE
1wd7
3d8n SAME PROTEIN COMPLEXED WITH LIGAND UP3
3d8r SAME PROTEIN COMPLEXED WITH PO4
3d8s SAME PROTEIN COMPLEXED WITH GLYCEROL