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Title :  2.35 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF A PUTATIVE TRNA (GUANINE-7-)-METHYLTRANSFERASE (TRMD) FROM STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MRSA252
 
Authors :  A. S. Halavaty, G. Minasov, J. Winsor, I. Dubrovska, L. Shuvalova, R. Se R. Zoraghi, N. Reiner, W. F. Anderson, Center For Structural Genom Infectious Diseases (Csgid)
Date :  04 Dec 09  (Deposition) - 22 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Putative Trna (Guanine-7-)-Methyltransferase, Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Methyltransferase, S-Adenosyl-L-Methionine, Transferase, Trna Processing, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, G. Minasov, J. Winsor, I. Dubrovska, L. Shuvalova, R. See, R. Zoraghi, N. Reiner, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 35 Angstrom Resolution Crystal Structure Of A Putative Trna (Guanine-7-)-Methyltransferase (Trmd) From Staphylococcus Aureus Subsp. Aureus Mrsa252
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)CODONPLUS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SAR1216, TRMD
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 282458
    Strain: MRSA252
    Synonym: M1G-METHYLTRANSFERASE, TRNA [GM37] METHYLTRANSFERASE, PUTATIVE TRNA (GUANINE-7-)-METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1OCS2Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg A:181 -Pro A:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KY7)

(-) PROSITE Motifs  (0, 0)

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(-) 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:229
 aligned with TRMD_STAAR | Q6GHJ5 from UniProtKB/Swiss-Prot  Length:245

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           TRMD_STAAR     1 MKIDYLTLFPEMFDGVLNHSIMKRAQENNKLQINTVNFRDYAINKHNQVDDYPYGGGQGMVLKPEPVFNAMEDLDVTEQARVILMCPQGEPFSHQKAVELSKADHIVFICGHYEGYDERIRTHLVTDEISMGDYVLTGGELPAMTMTDAIVRLIPGVLGNEQSHQDDSFSDGLLEFPQYTRPREFKGLTVPDVLLSGNHANIDAWRHEQKLIRTYNKRPDLIEKYPLTNADKQILERYKIGLK 243
               SCOP domains d3ky7a_ A: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------tRNA_m1G_MT-3ky7A01 A :22-219                                                                                                                                                                         ------------------------ Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhh.hhhhhhh...eeeeee.hhhh-......ee.........eehhhhhhhhhhhh......eeeee....ee.hhhhhhhhh...eeeee.......hhhhhhhh..eeee........hhhhhhhhhhhhhh....-------------..............ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ky7 A   1 MKIDYLTLFPEMFDGVLNHSIMKRAQENNKLQINTVNFRDYA-NKHNQVDDYPYGGGQGMVLKPEPVFNAMEDLDVTEQARVILMcPQGEPFSHQKAVELSKADHIVFICGHYEGYDERIRTHLVTDEISMGDYVLTGGELPAMTMTDAIVRLIPG-------------SDGLLEFPQYTRPREFKGLTVPDVLLSGNHANIDAWRHEQKLIRTYNKRPDLIEKYPLTNADKQILERYKIGLK 243
                                    10        20        30        40 | |    50        60        70        80     |  90       100       110       120       130       140       150     |   -       170       180       190       200       210       220       230       240   
                                                                    42 |                                        86-OCS                                                               156           170                                                                         
                                                                      44
   Legend:   → Mismatch (orange background)
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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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KY7)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: SPOUT (28)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRMD_STAAR | Q6GHJ5)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0052906    tRNA (guanine(37)-N(1))-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + guanine(37) in tRNA = N(1)-methylguanine(37) in tRNA + S-adenosyl-L-homocysteine.
    GO:0009019    tRNA (guanine-N1-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing N1-methylguanine.
    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:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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