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(-) Description

Title :  CHARACTERIZATION OF A TRIFUNCTIONAL MIMIVIRUS MRNA CAPPING ENZYME AND CRYSTAL STRUCTURE OF THE RNA TRIPHOSPHATASE DOMAINM.
 
Authors :  S. Shuman, D. Benarroch, P. Smith
Date :  13 Aug 07  (Deposition) - 01 Apr 08  (Release) - 01 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Mrna Capping, Phosphatase, Beta Tunnel, Viral Protein, Hydrolase, Mrna Processing, Multifunctional Enzyme, Nucleotidyltransferase, S-Adenosyl-L-Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Benarroch, P. Smith, S. Shuman
Characterization Of A Trifunctional Mimivirus Mrna Capping Enzyme And Crystal Structure Of The Rna Triphosphatase Domain.
Structure V. 16 501 2008
PubMed-ID: 18400173  |  Reference-DOI: 10.1016/J.STR.2008.01.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROBABLE MRNA-CAPPING ENZYME
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3) CODON+
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneREFSEQ YP_142736
    Organism ScientificMIMIVIRUS
    Organism Taxid315393

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FLC1Ligand/IonCITRATE ANION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FLC-1Ligand/IonCITRATE ANION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2FLC1Ligand/IonCITRATE ANION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:78 , ASP A:80 , TYR A:126 , PRO A:162BINDING SITE FOR RESIDUE ACT A 1002
2AC2SOFTWAREARG A:129 , LYS A:175 , HOH A:1096 , HOH A:1220 , HOH A:1224BINDING SITE FOR RESIDUE ACT A 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QY2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QY2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QY2)

(-) Exons   (0, 0)

(no "Exon" information available for 2QY2)

(-) 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:224
 aligned with MCE_MIMIV | Q5UQX1 from UniProtKB/Swiss-Prot  Length:1170

    Alignment length:227
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           MCE_MIMIV     11 DITIFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKNRGSGKLIGIDNWAITIKSTEEIPLVAGKSKISKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD  237
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhh..hhhhhhhhhh.......eeeeeeeeeeeeeeeehhh.eeeeeeeeeee..---...........eeeeeeeeeeeeeee..eeeeeeeeeee....hhhhh..eeeeeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qy2 A   11 DITIFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKNRGSGKLIGIDNWAITIKSTEEIPLVA---KISKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD  237
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150   |   160       170       180       190       200       210       220       230       
                                                                                                                                                                         154 158                                                                               

Chain B from PDB  Type:PROTEIN  Length:217
 aligned with MCE_MIMIV | Q5UQX1 from UniProtKB/Swiss-Prot  Length:1170

    Alignment length:224
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    
           MCE_MIMIV     14 IFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKNRGSGKLIGIDNWAITIKSTEEIPLVAGKSKISKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD  237
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) mRNA_triPase-2qy2B01 B:1014-1215                                                                                                                                                                          ---------------------- Pfam domains (1)
           Pfam domains (2) mRNA_triPase-2qy2B02 B:1014-1215                                                                                                                                                                          ---------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhh....hhhhhhhhhh.....eeeeee.-....eeee....eeeeeeeeee..------.........eeeeeeeeeeeee....eeeeeeeeeee.hhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2qy2 B 1014 IFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKN-GSGKLIGIDNWAITIKSTEEIPLV------SKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD 1237
                                  1023      1033      1043      1053      1063      1073      1083      1093      1103      1113      1123    | 1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233    
                                                                                                                                           1128 |                   1153   1160                                                                             
                                                                                                                                             1130                                                                                                           

   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 2QY2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QY2)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: CYTH (6)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MCE_MIMIV | Q5UQX1)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    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:0004484    mRNA guanylyltransferase activity    Catalysis of the reaction: GTP + (5')pp-Pur-mRNA = diphosphate + G(5')ppp-Pur-mRNA; G(5')ppp-Pur-mRNA is mRNA containing a guanosine residue linked 5' through three phosphates to the 5' position of the terminal residue.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0004651    polynucleotide 5'-phosphatase activity    Catalysis of the reaction: 5'-phosphopolynucleotide + H2O = polynucleotide + phosphate.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0098507    polynucleotide 5' dephosphorylation    The process of removing one or more phosphate groups from the 5' end of a polynucleotide.
cellular component
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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        MCE_MIMIV | Q5UQX12qze 3bgy

(-) Related Entries Specified in the PDB File

2qze 3bgy