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(-) Description

Title :  CRYSTAL STRUCTURE OF ARCHAEAL TRNA-METHYLASE FOR POSITION 56 (ATRM56) FROM PYROCOCCUS HORIKOSHII, COMPLEXED WITH S-ADENOSYL-L-METHIONINE
 
Authors :  M. Kuratani, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 Apr 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.48
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Deep Trefoil Knot, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kuratani, Y. Bessho, M. Nishimoto, H. Grosjean, S. Yokoyama
Crystal Structure And Mutational Study Of A Unique Spou Family Archaeal Methylase That Forms 2'-O-Methylcytidine At Position 56 Of Trna
J. Mol. Biol. V. 375 1064 2008
PubMed-ID: 18068186  |  Reference-DOI: 10.1016/J.JMB.2007.11.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UPF0106 PROTEIN PH0461
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-195
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: ATRM56

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MTA1Ligand/Ion5'-DEOXY-5'-METHYLTHIOADENOSINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:80 , THR B:81 , MET B:82 , GLY B:109 , ALA B:110 , LYS B:112 , ILE B:127 , GLY B:128 , GLN B:130 , HIS B:132 , SER B:133 , GLU B:134 , ALA B:137BINDING SITE FOR RESIDUE SAM B 500
2AC2SOFTWARELEU A:80 , THR A:81 , MET A:82 , GLY A:109 , ALA A:110 , GLU A:111 , ALA A:126 , ILE A:127 , GLY A:128 , GLN A:130 , HIS A:132 , GLU A:134 , ALA A:137BINDING SITE FOR RESIDUE MTA A 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2YY8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2YY8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YY8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2YY8)

(-) Exons   (0, 0)

(no "Exon" information available for 2YY8)

(-) 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:174
 aligned with TRM56_PYRHO | O58214 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:175
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
          TRM56_PYRHO     1 MIVVLRLGHRPERDKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDVVKRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKKGEDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKGLKKEFKGAKIKIVPQARGKKVVEVQ 175
               SCOP domains d2yy8a_ A: a utomated matches                                                                                                                                                   SCOP domains
               CATH domains 2yy8A00 A:1- 175  [code=3.40.1280.10, no name defined]                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......-.hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh.........hhhhhhhhh..eeeee....eehhhhhhhhhhhhhh...eeeee.....hhhhhhhh.eeee......hhhhhhhhhhhhhh.hhhhhh......eee........eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2yy8 A   1 MIVVLRLGHRPE-DKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDVVKRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKKGEDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKGLKKEFKGAKIKIVPQARGKKVVEVQ 175
                                    10 | |    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170     
                                      12 |                                                                                                                                                                 
                                        14                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:174
 aligned with TRM56_PYRHO | O58214 from UniProtKB/Swiss-Prot  Length:203

    Alignment length:174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    
          TRM56_PYRHO     1 MIVVLRLGHRPERDKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDVVKRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKKGEDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKGLKKEFKGAKIKIVPQARGKKVVEV 174
               SCOP domains d2yy8b_ B: automated matches                                                                                                                                                   SCOP domains
               CATH domains 2yy8B00 B:1-174  [code=3.40.1280.10, no name defined]                                                                                                                          CATH domains
           Pfam domains (1) -----------------------------------------------------Trm56-2yy8B01 B:54-174                                                                                                    Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------Trm56-2yy8B02 B:54-174                                                                                                    Pfam domains (2)
         Sec.struct. author .eeeee...hhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhh...eeee..hhhhhhhhh..eeeee....ee...hhhhhhhhhhh...eeeee.....hhhhhhhh.eeee......hhhhhhhhhhhhhhh.hhhhh......eee........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2yy8 B   1 MIVVLRLGHRPERDKRVTTHVALTARAFGADGIIIASEEDEKVKESVEDVVKRWGGPFFIEFNRNWRKVMKEFTGVKVHLTMYGLHVDDVIEELKEKLKKGEDFMIIVGAEKVPREVYELADYNVAIGNQPHSEVAALAVLLDRLLEGKGLKKEFKGAKIKIVPQARGKKVVEV 174
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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, 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: SPOUT (28)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRM56_PYRHO | O58214)
molecular function
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0008175    tRNA methyltransferase activity    Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in a tRNA 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:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0002128    tRNA nucleoside ribose methylation    The process that results in the modification of the sugar of a nucleoside in tRNA at the 2'O position.
    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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