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(-) Description

Title :  CRYSTAL STRUCTURE OF MRNA CAP GUANINE-N7 METHYLTRANSFERASE OBTAINED BY LIMITED PROTEOLYSIS
 
Authors :  P. Petit, V. H. Cowling
Date :  15 Oct 15  (Deposition) - 13 Jul 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Mrna Capping, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Varshney, A. P. Petit, J. A. Bueren-Calabuig, C. Jansen, D. A. Fletcher, M. Peggie, S. Weidlich, P. Scullion, A. V. Pisliakov, V. H. Cowling
Molecular Basis Of Rna Guanine-7 Methyltransferase (Rnmt) Activation By Ram.
Nucleic Acids Res. V. 44 10423 2016
PubMed-ID: 27422871  |  Reference-DOI: 10.1093/NAR/GKW637

(-) Compounds

Molecule 1 - MRNA CAP GUANINE-N7 METHYLTRANSFERASE
    ChainsA, B, C, D
    EC Number2.1.1.56
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 165-476
    GeneRNMT, KIAA0398
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRG7MT1,MRNA (GUANINE-N(7)-)-METHYLTRANSFERASE,MRNA CAP METHYLTRANSFERASE,HCM1P

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:180 , GLY A:205 , CYS A:206 , GLY A:207 , ASP A:227 , ILE A:228 , ASP A:261 , SER A:262 , GLN A:284 , PHE A:285 , VAL A:286 , TYR A:289 , HOH A:609 , HOH A:615 , HOH A:623 , HOH A:634binding site for residue SAH A 500
2AC2SOFTWARELYS B:180 , GLY B:205 , CYS B:206 , GLY B:207 , ASP B:227 , ILE B:228 , ASP B:261 , SER B:262 , GLN B:284 , PHE B:285 , VAL B:286 , TYR B:289 , HOH B:607 , HOH B:623 , HOH B:634 , HOH B:635 , HOH B:640 , HOH B:646 , HOH B:655binding site for residue SAH B 501
3AC3SOFTWARELYS C:180 , GLY C:205 , CYS C:206 , GLY C:207 , ASP C:227 , ILE C:228 , ASP C:261 , SER C:262 , GLN C:284 , PHE C:285 , VAL C:286 , TYR C:289 , HOH C:612 , HOH C:613 , HOH C:627 , HOH C:629binding site for residue SAH C 501
4AC4SOFTWARELYS D:180 , GLY D:205 , GLY D:207 , ASP D:227 , ILE D:228 , ASP D:261 , SER D:262 , GLN D:284 , PHE D:285 , VAL D:286 , TYR D:289 , HOH D:616 , HOH D:619 , HOH D:644 , HOH D:647 , HOH D:662binding site for residue SAH D 501
5AC5SOFTWAREARG B:272 , PHE C:170 , ASN C:174 , ASP C:242 , LYS C:244 , ASN C:245 , ARG C:247 , LEU C:412 , LYS C:413 , ARG C:414 , MET C:415 , PHE D:170 , TYR D:171 , ASP D:242 , MET D:243 , LYS D:244 , ASN D:245 , ARG D:247 , ASP D:248 , SER D:249 , LEU D:412 , LYS D:413 , ARG D:414 , MET D:415binding site for Di-peptide ARG C 246 and GLN D 416

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E9W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E9W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E9W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E9W)

(-) Exons   (0, 0)

(no "Exon" information available for 5E9W)

(-) 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:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh........eeeeee......hhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhhhhh...eee...eeeee...........eeeeee..eeee..hhhhhhhhhh...eeeeeeeehhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9w A 167 SRIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRRDSEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLEDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQLPLGTLSKSEWEATSIYLVFAFEKQQ 476
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      |369       379       389       399       409      |453       463       473   
                                                                                                                                                                                                                              363|                                              416|                         
                                                                                                                                                                                                                               367                                               451                         

Chain B from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh........eeeeee......hhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhhhhh...eee....eeee...........eeeee...eeee..hhhhhhhhhh...eeeeeeeehhhhhhhhh.hhhhhhhhhhh........hhhhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9w B 168 RIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRRDSEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLEDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQRLPLGTLSKSEWEATSIYLVFAFEKQQ 476
                                   177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357     ||370       380       390       400       410     ||453       463       473   
                                                                                                                                                                                                                             363|                                              416|                          
                                                                                                                                                                                                                              367                                               450                          

Chain C from PDB  Type:PROTEIN  Length:273
                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh........eeeeee......hhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhhhhh...eee...eeeee...........eeeeee..eeee..hhhhhhhhhhh..eeeeeeeehhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9w C 167 SRIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRRDSEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLEDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQLPLGTLSKSEWEATSIYLVFAFEKQQ 476
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      |369       379       389       399       409      |453       463       473   
                                                                                                                                                                                                                              363|                                              416|                         
                                                                                                                                                                                                                               367                                               451                         

Chain D from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhh........eeeeee......hhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhhhhh...eee...eeeee...........eeeeee....ee..hhhhhhhhhh...eeeeeeeehhhhhhhhh.hhhhhhhhhhh........hhhhhhhhh.eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e9w D 167 SRIFYLRNFNNWMKSVLIGEFLEKVRQKKKRDITVLDLGCGKGGDLLKWKKGRINKLVCTDIADVSVKQCQQRYEDMKNRRDSEYIFSAEFITADSSKELLIDKFRDPQMCFDICSCQFVCHYSFESYEQADMMLRNACERLSPGGYFIGTTPNSFELIRRLEASETESFGNEIYTVKFQKKGDYPLFGCKYDFNLEDVPEFLVYFPLLNEMAKKYNMKLVYKKTFLEFYEEKIKNNENKMLLKRMQRLPLGTLSKSEWEATSIYLVFAFEKQQ 476
                                   176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356      |369       379       389       399       409      |452       462       472    
                                                                                                                                                                                                                              363|                                              416|                          
                                                                                                                                                                                                                               367                                               450                          

   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 5E9W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E9W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E9W)

(-) Gene Ontology  (15, 15)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MCES_HUMAN | O431483bgv 3epp 5e8j 5e9j

(-) Related Entries Specified in the PDB File

5e8j 5E8J CONTAINS RNMT IN COMPLEX WITH RAM