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(-) Description

Title :  CRYSTAL STRUCTURE OF UROPORPHYRIN-III-C-METHYLTRANSFERASE FROM THERMUS THERMOPHILUS
 
Authors :  J. Jeyakanthan, T. H. Tahirov, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Mar 04  (Deposition) - 12 Apr 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Porphyrin, Methyltransferase, Heme, Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeyakanthan, T. H. Tahirov
Crystal Structure Of Uroporphyrin-Iii-C-Methyltrans From Thermus Thermophilus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UROPORPHYRIN-III C-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.107
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1VE2)

(-) Sites  (0, 0)

(no "Site" information available for 1VE2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VE2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Leu A:203 -Pro A:204
2Ser A:212 -Pro A:213
3Leu B:203 -Pro B:204
4Ser B:212 -Pro B:213

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VE2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VE2)

(-) Exons   (0, 0)

(no "Exon" information available for 1VE2)

(-) 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:222
 aligned with Q53WA2_THET8 | Q53WA2 from UniProtKB/TrEMBL  Length:235

    Alignment length:235
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230     
         Q53WA2_THET8     1 MRGKVYLVGAGFGGPEHLTLKALRVLEVAEVVLHDRLVHPGVLALAKGELVPVGKEGYGGKTPQEAITARLIALAREGRVVARLKGGDPMVFGRGGEEALALRRAGIPFEVVPGVTSAVGALSALGLPLTHRGLARSFAVATGHDPALPLPRADTLVLLMPLHTLGGLKERLLERFPPETPLALLARVGWPGEAVRLGRVEDLPGLGEGLPSPALLVVGKVVGLYGELLPKDHGL 235
               SCOP domains d1ve2a1 A:1-235 Uroporphyrin-III C-methyltransferase        (SUMT, UROM, CobA)                                                                                                                                                              SCOP domains
               CATH domains 1ve2A01 A:1-116 Cobalt-precorrin-4 Transmethylase; Do       main 1                                                  --------------------------------------------      --------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhhhhhhhhhh.eeeee...hhhhhh....eeeee-------..hhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhh..eeee.....hhhhhhhh............eeeee............eeeee.------hhhhhhhh......eeeeee.......eeeeee.hhh..........eeeee.hhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ve2 A   1 MRGKVYLVGAGFGGPEHLTLKALRVLEVAEVVLHDRLVHPGVLALAKGELVPV-------KTPQEAITARLIALAREGRVVARLKGGDPMVFGRGGEEALALRRAGIPFEVVPGVTSAVGALSALGLPLTHRGLARSFAVATGHDPALPLPRADTLVLLM------GLKERLLERFPPETPLALLARVGWPGEAVRLGRVEDLPGLGEGLPSPALLVVGKVVGLYGELLPKDHGL 235
                                    10        20        30        40        50  |      -|       70        80        90       100       110       120       130       140       150       160      |170       180       190       200       210       220       230     
                                                                               53      61                                                                                                160    167                                                                    


Chain B from PDB  Type:PROTEIN  Length:220
 aligned with Q53WA2_THET8 | Q53WA2 from UniProtKB/TrEMBL  Length:235

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
         Q53WA2_THET8     2 RGKVYLVGAGFGGPEHLTLKALRVLEVAEVVLHDRLVHPGVLALAKGELVPVGKEGYGGKTPQEAITARLIALAREGRVVARLKGGDPMVFGRGGEEALALRRAGIPFEVVPGVTSAVGALSALGLPLTHRGLARSFAVATGHDPALPLPRADTLVLLMPLHTLGGLKERLLERFPPETPLALLARVGWPGEAVRLGRVEDLPGLGEGLPSPALLVVGKVVGLYGELLPK 231
               SCOP domains d1ve2b_ B: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains 1ve2B01 B:2-116 Cobalt-precorrin-4 Transmethylase; D          omain 1                                              ------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --TP_methylase-1ve2B01 B:4-204                                                                                                                                                                             --------------------------- Pfam domains (1)
           Pfam domains (2) --TP_methylase-1ve2B02 B:4-204                                                                                                                                                                             --------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee....hhhhhhhhhhhhhhhh.eeee....hhhhhh....eeee.----------hhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhh...eeee...hhhhhhhhhh...........eeeeee............eeeee.hhhhhhhhhhhhhh......eeeeee.......eeeeee.hhhhhhhh.....eeeee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ve2 B   2 RGKVYLVGAGFGGPEHLTLKALRVLEVAEVVLHDRLVHPGVLALAKGELVPV----------QEAITARLIALAREGRVVARLKGGDPMVFGRGGEEALALRRAGIPFEVVPGVTSAVGALSALGLPLTHRGLARSFAVATGHDPALPLPRADTLVLLMPLHTLGGLKERLLERFPPETPLALLARVGWPGEAVRLGRVEDLPGLGEGLPSPALLVVGKVVGLYGELLPK 231
                                    11        21        31        41        51 |       -  |     71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
                                                                              53         64
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 2)

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, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: TP_methylase] (35)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q53WA2_THET8 | Q53WA2)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.

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  Cis Peptide Bonds
    Leu A:203 - Pro A:204   [ RasMol ]  
    Leu B:203 - Pro B:204   [ RasMol ]  
    Ser A:212 - Pro A:213   [ RasMol ]  
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