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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ADOMET DEPENDENT METHYLTRANSFERASE
 
Authors :  A. Gupta, P. H. Kumar, T. K. Dineshkumar, U. Varshney, H. S. Subramanya, Structural Genomics Consortium (Tbsgc)
Date :  20 Mar 01  (Deposition) - 26 Sep 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (4x)
Keywords :  Mycobacterium, Mtase, Adomet, Crystal, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Gupta, P. H. Kumar, T. K. Dineshkumar, U. Varshney, H. S. Subramanya
Crystal Structure Of Rv2118C: An Adomet-Dependent Methyltransferase From Mycobacterium Tuberculosis H37Rv.
J. Mol. Biol. V. 312 381 2001
PubMed-ID: 11554794  |  Reference-DOI: 10.1006/JMBI.2001.4935

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN RV2118C
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPQE60
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneRV2118C
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (4x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SAM4Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:81 , VAL A:82 , ILE A:83 , GLY A:107 , ALA A:108 , GLY A:109 , SER A:110 , GLY A:111 , ALA A:112 , LEU A:113 , GLU A:131 , GLN A:132 , ARG A:133 , HIS A:136 , SER A:160 , ASP A:161 , LEU A:162 , ASP A:178 , MET A:179 , VAL A:185 , HOH A:337 , HOH A:386 , HOH A:389 , HOH A:405BINDING SITE FOR RESIDUE SAM A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I9G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1I9G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I9G)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_TRM61PS51620 tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.TRMI_MYCTO10-261  1A:10-261
TRMI_MYCTU10-261  1A:10-261
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_TRM61PS51620 tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.TRMI_MYCTO10-261  1A:10-261
TRMI_MYCTU10-261  1A:10-261
Biological Unit 2 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_TRM61PS51620 tRNA (adenine(57)-N(1)/adenine(58)-N(1) or adenine(58)-N(1)) (EC 2.1.1.219 or EC 2.1.1.220) family profile.TRMI_MYCTO10-261  4A:10-261
TRMI_MYCTU10-261  4A:10-261

(-) Exons   (0, 0)

(no "Exon" information available for 1I9G)

(-) 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:264
 aligned with TRMI_MYCTO | P9WFZ0 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:264
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
           TRMI_MYCTO     4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVA 267
               SCOP domains d1i9ga_ A: Probable methyltransferase Rv2118c                                                                                                                                                                                                                            SCOP domains
               CATH domains 1i9gA01 A:4-67  [code=3.10.330.20, no name defined]             1i9gA02 A:68-231,A:248-267 Vaccinia Virus protein VP39                                                                                                              ----------------1i9gA02              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee....eeeee.....eeee..eeeehhhhh.....eeee.....eeeee..hhhhhhh.........hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh.....eeee..hhhhh......eeeeeee..hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhhh.....eee......eeee..eeee.........eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------SAM_TRM61  PDB: A:10-261 UniProt: 10-261                                                                                                                                                                                                                    ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1i9g A   4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVA 267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    

Chain A from PDB  Type:PROTEIN  Length:264
 aligned with TRMI_MYCTU | P9WFZ1 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:264
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    
           TRMI_MYCTU     4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVA 267
               SCOP domains d1i9ga_ A: Probable methyltransferase Rv2118c                                                                                                                                                                                                                            SCOP domains
               CATH domains 1i9gA01 A:4-67  [code=3.10.330.20, no name defined]             1i9gA02 A:68-231,A:248-267 Vaccinia Virus protein VP39                                                                                                              ----------------1i9gA02              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee....eeeee.....eeee..eeeehhhhh.....eeee.....eeeee..hhhhhhh.........hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhh.....eeee..hhhhh......eeeeeee..hhhhhhhhhhhheeeeeeeeeee.hhhhhhhhhhhhhhhh.....eee......eeee..eeee.........eeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) ------SAM_TRM61  PDB: A:10-261 UniProt: 10-261                                                                                                                                                                                                                    ------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1i9g A   4 TGPFSIGERVQLTDAKGRRYTMSLTPGAEFHTHRGSIAHDAVIGLEQGSVVKSSNGALFLVLRPLLVDYVMSMPRGPQVIYPKDAAQIVHEGDIFPGARVLEAGAGSGALTLSLLRAVGPAGQVISYEQRADHAEHARRNVSGCYGQPPDNWRLVVSDLADSELPDGSVDRAVLDMLAPWEVLDAVSRLLVAGGVLMVYVATVTQLSRIVEALRAKQCWTEPRAWETLQRGWNVVGLAVRPQHSMRGHTAFLVATRRLAPGAVA 267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I9G)

(-) Gene Ontology  (9, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRMI_MYCTO | P9WFZ0)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016429    tRNA (adenine-N1-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methyladenine.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0031515    tRNA (m1A) methyltransferase complex    A protein complex involved in the catalysis of the formation of the modified nucleotide 1-methyladenosine (m1A) in tRNA. In yeast, it is a heterotetramer of two subunits, Gcd10p and Gcd14p, while in bacteria and archaea it is a homotetramer.

Chain A   (TRMI_MYCTU | P9WFZ1)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016429    tRNA (adenine-N1-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methyladenine.
    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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031515    tRNA (m1A) methyltransferase complex    A protein complex involved in the catalysis of the formation of the modified nucleotide 1-methyladenosine (m1A) in tRNA. In yeast, it is a heterotetramer of two subunits, Gcd10p and Gcd14p, while in bacteria and archaea it is a homotetramer.

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