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(-) Description

Title :  TRMH
 
Authors :  O. Nureki, K. Watanabe, S. Fukai, R. Ishii, Y. Endo, H. Hori, S. Yokoyama Structural Genomics/Proteomics Initiative (Rsgi)
Date :  17 Oct 03  (Deposition) - 04 May 04  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Deep Trefoil Knot, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Nureki, K. Watanabe, S. Fukai, R. Ishii, Y. Endo, H. Hori, S. Yokoyam
Deep Knot Structure For Construction Of Active Site And Cofactor Binding Site Of Trna Modification Enzyme
Structure V. 12 593 2004
PubMed-ID: 15062082  |  Reference-DOI: 10.1016/J.STR.2004.03.003

(-) Compounds

Molecule 1 - TRNA (GM18) METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.34
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACUROVIRUS
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 274

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
2SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:32 , HIS A:34 , ASN A:35 , ARG A:41 , GLU A:65 , THR A:66 , GLU A:124 , ASN A:152 , HOH A:419 , HOH A:464BINDING SITE FOR RESIDUE PO4 A 201
2AC2SOFTWAREARG A:9 , GLU A:13 , ASN A:29 , HIS A:31 , ASN A:55 , GLY A:58 , HOH A:408 , HOH A:483BINDING SITE FOR RESIDUE PO4 A 202
3AC3SOFTWAREARG A:41 , THR A:99 , PHE A:121 , GLY A:122 , ALA A:123 , GLU A:124 , LYS A:125 , TRP A:126 , GLY A:127 , ILE A:142 , MET A:144 , LEU A:151 , VAL A:153 , ALA A:156 , HOH A:442 , HOH A:561 , HOH A:568 , HOH A:583BINDING SITE FOR RESIDUE SAM A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1V2X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V2X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V2X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V2X)

(-) Exons   (0, 0)

(no "Exon" information available for 1V2X)

(-) 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:191
 aligned with TRMH_THET8 | Q5SM16 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           TRMH_THET8     1 MRERTEARRRRIEEVLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQRQRLKAGLYDRPRLDPELYQKVLADW 191
               SCOP domains d1v2xa_ A: tRNA (Gm18) methyltransferase TrmH                                                                                                                                                   SCOP domains
               CATH domains 1v2xA00 A:1-191  [code=3.40.1280.10, no name defined]                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhh...eeeee.hhhhh........hhhhh.eeeee.hhhhhhhhhhhh..eeeee......ee.hhh.....eeeee.......hhhhhhhh.eeee..........hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v2x A   1 MRERTEARRRRIEEVLRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGAEKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQRQRLKAGLYDRPRLDPELYQKVLADW 191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V2X)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRMH_THET8 | Q5SM16)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008173    RNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0009020    tRNA (guanosine-2'-O-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA = S-adenosyl-L-homocysteine + tRNA containing 2'-O-methylguanosine.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0002938    tRNA guanine ribose methylation    The process whereby a guanosine residue in a tRNA is methylated on the 2'-hydroxyl group of the ribose moiety.
    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.

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  1v2x
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