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(-) Description

Title :  STRUCTURE AND MECHANISM OF MRNA CAP (GUANINE N-7) METHYLTRANSFERASE
 
Authors :  C. Fabrega, S. Hausmann, V. Shen, S. Shuman, C. D. Lima
Date :  16 Nov 03  (Deposition) - 03 Feb 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Methyltransferase, Rna, Cap, M7G, Messenger Rna Cap (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Fabrega, S. Hausmann, V. Shen, S. Shuman, C. D. Lima
Structure And Mechanism Of Mrna Cap (Guanine-N7) Methyltransferase
Mol. Cell V. 13 77 2004
PubMed-ID: 14731396  |  Reference-DOI: 10.1016/S1097-2765(03)00522-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MRNA CAPPING ENZYME
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSUMO-SMT3
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ECU10_0380
    Organism Scientific: ENCEPHALITOZOON CUNICULI
    Organism Taxid: 6035
    Synonym: MRNA CAP (GUANINE N-7) METHYLTRANSFERASE ECM1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GTG1Ligand/Ion7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:54 , GLY A:72 , GLY A:74 , ASP A:94 , ILE A:95 , ASP A:122 , SER A:123 , TYR A:124 , GLN A:140 , PHE A:141 , SER A:142 , TYR A:145 , GTG A:300 , HOH A:303 , HOH A:308 , HOH A:315BINDING SITE FOR RESIDUE SAH A 299
2AC2SOFTWAREASN A:50 , ASN A:51 , LYS A:54 , LEU A:80 , LYS A:81 , ARG A:106 , TYR A:284 , SAH A:299 , HOH A:314 , HOH A:318 , HOH A:336 , HOH A:347BINDING SITE FOR RESIDUE GTG A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RI1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RI1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RI1)

(-) Exons   (0, 0)

(no "Exon" information available for 1RI1)

(-) 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:252
 aligned with MCES_ENCCU | Q8SR66 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:252
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275  
           MCES_ENCCU    26 SKTINIRNANNFIKACLIRLYTKRGDSVLDLGCGKGGDLLKYERAGIGEYYGVDIAEVSINDARVRARNMKRRFKVFFRAQDSYGRHMDLGKEFDVISSQFSFHYAFSTSESLDIAQRNIARHLRPGGYFIMTVPSRDVILERYKQGRMSNDFYKIELEKMEDVPMESVREYRFTLLDSVNNCIEYFVDFTRMVDGFKRLGLSLVERKGFIDFYEDEGRRNPELSKKMGLGCLTREESEVVGIYEVVVFRKL 277
               SCOP domains d1ri1a_ A: mRNA cap (Guanine N-7) methyltransferase                                                                                                                                                                                                          SCOP domains
               CATH domains 1ri1A00 A:41-292 Vaccinia Virus protein VP39                                                                                                                                                                                                                 CATH domains
               Pfam domains Pox_MCEL-1ri1A01 A:41-292                                                                                                                                                                                                                                    Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhh...eeeeee.hhhhhhhhhhhhhh.....eeeeee.............eeeeeee.hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeehhhhhhhhhhh.......eeee.......hhhhh.eeeeee......eeee..hhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ri1 A  41 SKTINIRNANNFIKACLIRLYTKRGDSVLDLGCGKGGDLLKYERAGIGEYYGVDIAEVSINDARVRARNMKRRFKVFFRAQDSYGRHMDLGKEFDVISSQFSFHYAFSTSESLDIAQRNIARHLRPGGYFIMTVPSRDVILERYKQGRMSNDFYKIELEKMEDVPMESVREYRFTLLDSVNNCIEYFVDFTRMVDGFKRLGLSLVERKGFIDFYEDEGRRNPELSKKMGLGCLTREESEVVGIYEVVVFRKL 292
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MCES_ENCCU | Q8SR66)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0004482    mRNA (guanine-N7-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + G(5')pppR-RNA = S-adenosyl-L-homocysteine + m7G(5')pppR-RNA. m7G(5')pppR-RNA is mRNA containing an N7-methylguanine cap; R may be guanosine or adenosine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor 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:0006370    7-methylguanosine mRNA capping    Addition of the 7-methylguanosine cap to the 5' end of a nascent messenger RNA transcript.
    GO:0036265    RNA (guanine-N7)-methylation    The addition of a methyl group to the N7 atom in the base portion of a guanine nucleotide residue in an RNA molecule.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MCES_ENCCU | Q8SR66: 1ri2 1ri3 1ri4 1ri5 1z3c 2hv9

(-) Related Entries Specified in the PDB File

1ri2 1ri3 1ri4 1ri5