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(-) Description

Title :  THERMUS THERMOPHILUS UROPORPHYRINOGEN III SYNTHASE
 
Authors :  H. L. Schubert
Date :  23 May 08  (Deposition) - 05 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
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 Uroporphyrinoge Iii Synthase-Product Complex.
Biochemistry V. 47 8648 2008
PubMed-ID: 18651750  |  Reference-DOI: 10.1021/BI800635Y

(-) Compounds

Molecule 1 - UROPORPHYRINOGEN-III SYNTHASE
    Chains: A
    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

  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
1AC1SOFTWARETHR A:59 , GLY A:60 , LYS A:92 , HOH A:342 , HOH A:367BINDING SITE FOR RESIDUE GOL A 254

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D8S)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:33 -Glu A:34
2Gln A:121 -Gly A:122
3Leu A:248 -Gln A:249

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D8S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D8S)

(-) Exons   (0, 0)

(no "Exon" information available for 3D8S)

(-) 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:250
 aligned with Q72KM1_THET2 | Q72KM1 from UniProtKB/TrEMBL  Length:253

    Alignment length:250
                             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     - -MRIAYAGLRRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQ 249
               SCOP domains d3d8sa_ A: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 3d8sA01 A:-1-35,A:157-249           3d8sA02 A:36-156  [code=3.40.50.10090, no name defined]                                                                  3d8sA01 A:-1-35,A:157-249  [code=3.40.50.10090, no name defined]                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhhhhhhhhh.eeeee........ee..hhhhhhhhhh....eeee.hhhhhhhhhhhhhhh...hhhhhhhheeee.hhhhhhhhhhh.....ee...hhhhhhhhh....eeeeee.....hhhhhhhhhhh.eeeeee..ee...hhhhhhhhhhhhhh....eeee.hhhhhhhhhhhh.hhhhhhhhhhh..eeeeehhhhhhhhhhh.....eee...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d8s A  -1 TMRIAYAGLRRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATTGVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLLPQGRGVAALQLYGKPLPLLENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLRGEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDETERLGSLLQGFKRALQ 249
                            ||       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
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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, 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  (0, 0)

(no "Pfam Domain" information available for 3D8S)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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  Cis Peptide Bonds
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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
        Q72KM1_THET2 | Q72KM1: 3d8n 3d8r 3d8t

(-) 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
3d8t APO PROTEIN