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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA GUANINE-N1-METHYLTRANSFERASE FROM BARTONELLA HENSELAE USING MPCS.
 
Authors :  T. E. Edwards, G. Stahl, C. J. Gerdts, B. L. Staker, Accelerated Technologies Center For Gene To 3D Structure (Atcg3D), Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Date :  22 Jul 09  (Deposition) - 11 Aug 09  (Release) - 22 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Niaid, Ssgcid, Seattle Structural Genomics Center For Infectious Diseases, Microcapillary Protein Crystallization System, Mpcs, Psi-2, Protein Structure Initiative, Accelerated Technologies Center For Gene To 3D Structure, Atcg3D, Cytoplasm, Methyltransferase, S-Adenosyl-L- Methionine, Transferase, Trna Processing, Protein Knot, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, G. Stahl, C. J. Gerdts, B. L. Staker, Accelerated Technologies Center For Gene To 3D Structure (Atcg3D), Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Crystal Structure Of Trna Guanine-N1-Methyltransferase From Bartonella Henselae Using Mpcs.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE
    Chains: A, B
    EC Number: 2.1.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBADSMT
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TRMD, BH15820
    Organism Common: ROCHALIMAEA HENSELAE
    Organism Scientific: BARTONELLA HENSELAE
    Organism Taxid: 38323
    Strain: HOUSTON-1
    Synonym: M1G-METHYLTRANSFERASE, TRNA [GM37] METHYLTRANSFERASE

 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 3IEF)

(-) Sites  (0, 0)

(no "Site" information available for 3IEF)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Phe A:15 -Pro A:16
2Arg A:181 -Pro A:182
3Phe B:15 -Pro B:16
4Arg B:181 -Pro B:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IEF)

(-) 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:224
 aligned with TRMD_BARHE | Q6G1R9 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:229
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         
           TRMD_BARHE     2 KFQARVLTLYPEMFPGFLGCSLAGQALKQGIWSLETVQIRDFALDKHHSVDDTPAGGGAGMVMRADVLAAALDSCPNDSPRLLMSPRGRLLNQAYARSLARSSGVTLVCGRFEGVDERIIEARELEEVSIGDYILSGGETAALVLLDAIVRLLPGVMGNEISAKCESFENGLLEHPQYTRPAVFEGRGIPPVLTSGHHKAIANWRQQQAESLTRQRRPDLYALYNKNRQ 230
               SCOP domains d3iefa_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains 3iefA01 A:2-167  [code=3.40.1280.10, no nam     e defined]                                                                                                            --------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh-----..ee.........eehhhhhhhhhh.......eeee....ee.hhhhhhhhh...eeeeee......hhhhhhhh..eeee.......hhhhhhhhhhhhhhh......hhhhh...hhhhhh...........ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ief A   2 KFQARVLTLYPEMFPGFLGCSLAGQALKQGIWSLETVQIRDFA-----SVDDTPAGGGAGMVMRADVLAAALDSCPNDSPRLLMSPRGRLLNQAYARSLARSSGVTLVCGRFEGVDERIIEARELEEVSIGDYILSGGETAALVLLDAIVRLLPGVMGNEISAKCESFENGLLEHPQYTRPAVFEGRGIPPVLTSGHHKAIANWRQQQAESLTRQRRPDLYALYNKNRQ 230
                                    11        21        31        41  |     51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221         
                                                                     44    50                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with TRMD_BARHE | Q6G1R9 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
           TRMD_BARHE     2 KFQARVLTLYPEMFPGFLGCSLAGQALKQGIWSLETVQIRDFALDKHHSVDDTPAGGGAGMVMRADVLAAALDSCPNDSPRLLMSPRGRLLNQAYARSLARSSGVTLVCGRFEGVDERIIEARELEEVSIGDYILSGGETAALVLLDAIVRLLPGVMGNEISAKCESFENGLLEHPQYTRPAVFEGRGIPPVLTSGHHKAIANWRQQQAESLTRQRRPDLYALYNKN 228
               SCOP domains d3iefb_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains 3iefB01 B:2-167  [code=3.40.1280.10, no name     defined]                                                                                                             ------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhhhhhhhhhhhhhhhhhhh...eeeeee.hhhh.----..ee.........eehhhhhhhhhhh......eeee....ee.hhhhhhhhhh..eeeeee......hhhhhhhh..eeee.......hhhhhhhhhhhhhhh....--------..hhhhhh...........ee..ee.hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ief B   2 KFQARVLTLYPEMFPGFLGCSLAGQALKQGIWSLETVQIRDFAL----SVDDTPAGGGAGMVMRADVLAAALDSCPNDSPRLLMSPRGRLLNQAYARSLARSSGVTLVCGRFEGVDERIIEARELEEVSIGDYILSGGETAALVLLDAIVRLLPG--------KCESFENGLLEHPQYTRPAVFEGRGIPPVLTSGHHKAIANWRQQQAESLTRQRRPDLYALYNKN 228
                                    11        21        31        41   |    51        61        71        81        91       101       111       121       131       141       151    |    -   |   171       181       191       201       211       221       
                                                                      45   50                                                                                                       156      165
   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, 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  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRMD_BARHE | Q6G1R9)
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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  Cis Peptide Bonds
    Arg A:181 - Pro A:182   [ RasMol ]  
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 Related Entries

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(-) Related Entries Specified in the PDB File

3e5y RNA METHYLTRANSFERASE FROM BURKHOLDERIA PSEUDOMALLEI RELATED ID: BAHEA.01015.A RELATED DB: TARGETDB