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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TWO-SUBUNIT TRNA M1A58 METHYLTRANSFERASE TRM6-TRM61 IN COMPLEX WITH SAM
 
Authors :  Y. Zhu, M. Wang, C. Wang, X. Fan, X. Jiang, M. Teng, X. Li
Date :  14 Nov 15  (Deposition) - 14 Sep 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Trna, Complex, Sam, Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Wang, Y. Zhu, C. Wang, X. Fan, X. Jiang, M. Ebrahimi, Z. Qiao, L. Niu, M. Teng, X. Li
Crystal Structure Of The Two-Subunit Trna M(1)A58 Methyltransferase Trm6-Trm61 From Saccharomyces Cerevisiae.
Sci Rep V. 6 32562 2016
PubMed-ID: 27582183  |  Reference-DOI: 10.1038/SREP32562

(-) Compounds

Molecule 1 - TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE NON-CATALYTIC SUBUNIT TRM6
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GCD10, TIF33, TRM6, YNL062C, N2422
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: GENERAL CONTROL NON-DEREPRESSIBLE PROTEIN 10,PROTEIN GCD10, TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRM6,TRNA(M1A58)MTASE SUBUNIT TRM6
 
Molecule 2 - TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE CATALYTIC SUBUNIT TRM61
    Chains: B
    EC Number: 2.1.1.220
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: GCD14, TRM61, YJL125C, J0710
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: GENERAL CONTROL NON-DEREPRESSIBLE PROTEIN 14,PROTEIN GCD14, TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRM61,TRNA(M1A58)MTASE SUBUNIT TRM61

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

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, 2)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:92 , VAL B:94 , GLY B:118 , THR B:119 , GLY B:120 , SER B:121 , GLY B:122 , SER B:123 , PHE B:124 , GLU B:139 , PHE B:140 , ARG B:144 , ARG B:167 , ASP B:168 , VAL B:169 , CYS B:170 , ASP B:203 , LEU B:204 , HOH B:506binding site for residue SAM B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ERG)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala B:117 -Gly B:118

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ERG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ERG)

(-) Exons   (0, 0)

(no "Exon" information available for 5ERG)

(-) 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:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.....eeeee.....eee.hhh.eee.hhh.......eeeee.....eeee...eeeee..hhhhhhhhhhhh.........hhhhhhhhhhhh......eeeeee...hhhhhhhhhhhhh.........eeeeee......hhhhhhh..hhhhhhhheeeeehhhhhh..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhh...eeeeeeeeeeeeeee......ee.........eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5erg A  -6 HHHSQDPMNALTTIDFNQHVIVRLPSKNYKIVELKPNTSVSLGKFGAFEVNDIIGYPFGLTFEIYYDPIGKVRLLSKYFTVEYLSSSNLLQFLIDKGDIQRVLDMSQESMGMLLNLANIQSEGNYLCMDETGGLLVYFLLERMFGGDNESKSKGKVIVIHENEHANLDLLKFANYSEKFIKEHVHTISLLDFFEPPTLQEIQSRFTPLPKEEARALKGGKKNSYYRKLRWYNTQWQILELTGEFLYDGLVMATTLHLPTLVPKLAEKIHGSRPIVCYGQFKETLLELAHTLYSDLRFLAPSILETRCRPYQSIRGKLHPLMTMKGGGGYLMWCHRVIPAP 452
                                     3        13        23        33        43        53      ||81     ||192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452
                                                                                             60|      87|                                                                                                                                                                                                                                                                       
                                                                                              79      189                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............eeeeeee..eeeeee.....eeee..eeee.hhh......eeeee...eeeeee..hhhhhhhhh.......hhhhhhhhhhhh......eeeee....hhhhhhhhhhh.eeeeee.hhhhhhhhhhhhhhh......eeeee.hhhhhh.........................eeee...hhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhhhhh..eeeeeeeeeeeeeeeeeee..hhhhhhhhhhhhhhh..........eeeeeee.........eeeeeee......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5erg B   4 NCFSGYKDLIKEGDLTLIWVSRDNIKPVRMHSEEVFNTRYGSFPHKDIIGKPYGSQIAIRTFAFVHVLQPTPELWTLSLPHRTQIVYTPDSSYIMQRLNCSPHSRVIEAGTGSGSFSHAFARSVGHLFSFEFHHIRYEQALEEFKEHGLIDDNVTITHRDVCQGGFLIKKGDTTSYEFGNNETAASLNANVVFLDLPAPWDAIPHLDSVISVDEKVGLCCFSPCIEQVDKTLDVLEKYGWTDVEMVEIQGRQYESRRQMVRSLNDALERLRDIKRHKIKEGDSNYKWKEVTKMEAEIKSHTSYLTFAFKVVNRSRDDEKVNEIL 378
                                    13        23        33        43        53        63||      78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278      |334       344       354       364       374    
                                                                                       64|                                                                                                                                                                                                                    285|                                              
                                                                                        70                                                                                                                                                                                                                     332
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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  (0, 0)

(no "SCOP Domain" information available for 5ERG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ERG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ERG)

(-) Gene Ontology  (10, 16)

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  TRM61_YEAST | P46959
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        TRM61_YEAST | P46959: 5eqj
        TRM6_YEAST | P41814: 5eqj

(-) Related Entries Specified in the PDB File

5eqj