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(-) Description

Title :  STRUCTURE OF AN ASYMMETRIC TETRAMER OF HUMAN TRNA M1A58 METHYLTRANSFERASE IN A COMPLEX WITH SAH AND TRNA3LYS
 
Authors :  J. Finer-Moore, N. Czudnochowski, J. D. O'Connell Iii, A. L. Wang, R. M
Date :  02 Jul 15  (Deposition) - 04 Nov 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym./Biol. Unit :  A,B,D,E,M,N
Keywords :  Class I Methyltransferase Fold, Trna Modification, Sam-Dependent Methyl Transfer, Transferase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Finer-Moore, N. Czudnochowski, J. D. O'Connell, A. L. Wang, R. M. Stroud
Crystal Structure Of The Human Trna M(1)A58 Methyltransferase-Trna3(Lys) Complex: Refolding Of Substrat Trna Allows Access To The Methylation Target.
J. Mol. Biol. V. 427 3862 2015
PubMed-ID: 26470919  |  Reference-DOI: 10.1016/J.JMB.2015.10.005

(-) Compounds

Molecule 1 - TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE CATALYTIC SUBUNIT TRMT61A
    Chains: A, D
    EC Number: 2.1.1.220
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Plasmid: PET17B-6HISTRM6-TRM61
    Expression System Taxid: 469008
    Gene: TRMT61A, C14ORF172, TRM61
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRMT61A,TRNA(M1A58) MTASE SUBUNIT TRMT61A
 
Molecule 2 - TRNA (ADENINE(58)-N(1))-METHYLTRANSFERASE NON-CATALYTIC SUBUNIT TRM6
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: BL21(DE3)
    Expression System Plasmid: PET17B-6HISTRM6-TRM61
    Expression System Taxid: 469008
    Gene: TRMT6, KIAA1153, TRM6, CGI-09
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TRNA(M1A58)-METHYLTRANSFERASE SUBUNIT TRM6,TRNA(M1A58)MTASE SUBUNIT TRM6
 
Molecule 3 - TRNA3LYS
    Chains: M, N
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABDEMN

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:84 , GLN A:85 , ILE A:86 , LEU A:87 , SER A:110 , GLY A:111 , THR A:112 , GLY A:115 , SER A:116 , VAL A:117 , GLU A:135 , PHE A:136 , ARG A:140 , ASP A:163 , VAL A:164 , ASP A:181 , ILE A:182 , PRO A:183 , C M:56binding site for residue SAH A 301
2AC2SOFTWARETHR D:84 , GLN D:85 , ILE D:86 , LEU D:87 , SER D:110 , GLY D:111 , THR D:112 , GLY D:115 , SER D:116 , VAL D:117 , GLU D:135 , PHE D:136 , ARG D:140 , ASP D:163 , VAL D:164 , ASP D:181 , ILE D:182 , C N:56binding site for residue SAH D 301
3AC3SOFTWAREU M:8 , A M:9 , U M:12binding site for residue NA M 101
4AC4SOFTWAREU N:8 , A N:9 , U N:12binding site for residue NA N 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CD1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ser A:110 -Gly A:111
2Ala A:126 -Pro A:127
3Ser D:110 -Gly D:111
4Ala D:126 -Pro D:127

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CD1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CD1)

(-) Exons   (0, 0)

(no "Exon" information available for 5CD1)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeee..eeeeee.....eee....eee......................eee..hhhhhhhhh.......hhhhhhhhhhhh......eeeee....hhhhhhhhhhhh...ee.....hhhhhhhhhhhhhhh.hhhhh.....hhhhhh........eeee...hhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh.eeeeeeeeeeeeeeeeee..............eeeeee...ee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cd1 A   2 SFVAYEELIKEGDTAILSLGHGAMVAVRVQRGAQTQTRHGVLRHSVDLIGRPFGSKVTCGRGGWVYVLHPTPELWTLNLPHRTQILYSTDIALITMMLELRPGSVVCESGTGSGSVSHAIIRTIAPTGHLHTVEFHQQRAEKAREEFQEHRVGRWVTVRTQDVCRSGFGVSHVADAVFLDIPSPWEAVGHAWDALKVEGGRFCSFSPCIEQVQRTCQALAARGFSELSTLEVLPQVYNVRTVSLPPPDLGTGDTSPFRSGTPMKEAVGHTGYLTFATKTPG 289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 ||    268       278       288 
                                                                                                                                                                                                                                                                                     253|                            
                                                                                                                                                                                                                                                                                      261                            


Chain B from PDB  Type:PROTEIN  Length:321
                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeeee......eee..eee............ee.................hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhh.......hhhhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eeeeee......hhhhhhhh.hhhhhh.eeeee..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhh.eeeeeeeeeeeeeee......eeeeee.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cd1 B  18 HRIRDGDFVVLKREDVFKAVQVQRRKKVTFEKQWFYLDNVIGHSYGTAFEVTSGGSLQPKTTFRDKTEFAQDKYIKKKKKKYEAIITVVKPSTRILSIMYYAREPGKINHMRYDTLAQMLTLGNIRAGNKMIVMETCAGLVLGAMMERMGGFGSIIQLYPGGGPVRAATACFGFPKSFLSGLYEFPLNKVDSLLHGTFSYIQEKQRRQEEQRKRHLEAAALLSERNADGLIVASRFHPTPLLLSLLDFVAPSRPFVVYCQYKEPLLECYTKLRERGGVINLRLSETWLRNYQVLPDRSHPKLLMSGGGGYLLSGFTVAMDN 463
                                    27        37        47        57        67        77|      142       152       162       172       182       192       202       212       222       232       242       252       262       342       352       362       372       382       392       402       412       422       432       442       452       462 
                                                                                      77|                                                                                                                                       271|                                                                                                                         
                                                                                      133                                                                                                                                        342                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.....eeeee.....eeee..eeeehhhhh.......eee.....eeeee..hhhhhh..........hhhhhhhhhhhh......eeeee.....hhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhh.hhh.ee....hhhhhh........eeee.......hhhhhhhhh....eee..ee.hhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee....................eee...eee...eeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cd1 D   2 SFVAYEELIKEGDTAILSLGHGAMVAVRVQRGAQTQTRHGVLRHSVDLIGRPFGSKVTCGRGGWVYVLHPTPELWTLNLPHRTQILYSTDIALITMMLELRPGSVVCESGTGSGSVSHAIIRTIAPTGHLHTVEFHQQRAEKAREEFQEHRVGRWVTVRTQDVCRSGFGVSHVADAVFLDIPSPWEAVGHAWDALKVEGGRFCSFSPCIEQVQRTCQALAARGFSELSTLEVLPQVYNVRTVSLPPPDLGTGDTSPFRSGTPMKEAVGHTGYLTFATKTPG 289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 ||    268       278       288 
                                                                                                                                                                                                                                                                                     253|                            
                                                                                                                                                                                                                                                                                      261                            


Chain E from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeeee.....eee....eee.hhhh......eeee....ee.........................hhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eeeeee......hhhhhh...hhhhhh.eeeee..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhh.eeeeeeeeeeeeeeeee..eeeeeeee.....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cd1 E  18 HRIRDGDFVVLKREDVFKAVQVQRRKKVTFEKQWFYLDNVIGHSYGTAFEVTSGGSLQPKKKEAGTDNRNIVDDGKSQKLTQDDIKALKDKGIKGEEIVQQLIENSTTFRDKTEFAQDKYIKKKKKKYEAIITVVKPSTRILSIMYYAREPGKINHMRYDTLAQMLTLGNIRAGNKMIVMETCAGLVLGAMMERMGGFGSIIQLYPGGGPVRAATACFGFPKSFLSGLYEFPLNKVDSLLHGTFSYIQEKQRRQEEQRKRHLEAAALLSERNADGLIVASRFHPTPLLLSLLDFVAPSRPFVVYCQYKEPLLECYTKLRERGGVINLRLSETWLRNYQVLPDRSHPKLLMSGGGGYLLSGFTVAMDN 463
                                    27        37        47        57        67        77||      96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266    || 346       356       366       376       386       396       406       416       426       436       446       456       
                                                                                       78|                                                                                                                                                                                    271|                                                                                                                         
                                                                                        88                                                                                                                                                                                     342                                                                                                                         


Chain M from PDB  Type:RNA  Length:74
                                                                                                          
                 5cd1 M   0 GGCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGCC  75
                                     9        19        29    ||  41        51        61        71    
                                                             34|                                      
                                                              37                                      


Chain N from PDB  Type:RNA  Length:76
                                                                                                            
                 5cd1 N   0 GGCCCGGAUAGCUCAGUCGGUAGAGCAUCAGACUUUUAAUCUGAGGGUCCAGGGUUCAAGUCCCUGUUCGGGCGCC  75
                                     9        19        29        39        49        59        69
   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  (0, 0)

(no "SCOP Domain" information available for 5CD1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CD1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CD1)

(-) Gene Ontology  (10, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  5cd1
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  TRM61_HUMAN | Q96FX7
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  TRM6_HUMAN | Q9UJA5
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  2.1.1.220
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 Related Entries

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

UniProtKB/Swiss-Prot
        TRM61_HUMAN | Q96FX7: 5ccb 5ccx
        TRM6_HUMAN | Q9UJA5: 5ccb 5ccx

(-) Related Entries Specified in the PDB File

5ccb 5ccx