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(-) Description

Title :  TRICLINIC STRUCTURE OF MIMIVIRUS CAPPING ENZYME TRIPHOSPHATASE AT 1.65 A
 
Authors :  P. Smith, D. Bennaroch, S. Shuman
Date :  27 Nov 07  (Deposition) - 01 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rna Capping, Tunnel Triphsophatase, Metalloenzyme, Beta Barrel, Hydrolase, Mrna Capping, Mrna Processing, Multifunctional Enzyme, Nucleotidyltransferase, S-Adenosyl- L-Methionine, Transferase, Virion, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Benarroch, P. Smith, S. Shuman
Triclinic Structure Of Mimivirus Capping Enzyme Triphosphatase At 1. 65 A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYNUCLEOTIDE 5'-TRIPHOSPHATASE
    ChainsA, B
    EC Number3.1.3.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A-SMT3
    Expression System StrainBL21(DE3)CODON PLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-237
    GeneYP_142736
    Organism ScientificACANTHAMOEBA POLYPHAGA MIMIVIRUS
    Organism Taxid212035

 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  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:1127 , ARG B:1129 , ARG B:1177 , GLU B:1210 , GLU B:1212 , HOH B:3164 , HOH B:3172BINDING SITE FOR RESIDUE ACT B 2001
2AC2SOFTWAREGLU B:1039 , GLU B:1149 , ARG B:1177 , GLU B:1214 , HOH B:3058 , HOH B:3181BINDING SITE FOR RESIDUE ACT B 2002
3AC3SOFTWAREGLU A:17 , SER A:68 , ASN A:70 , TYR A:178 , HOH A:3295 , HOH A:3310BINDING SITE FOR RESIDUE ACT A 2003
4AC4SOFTWARETYR A:47 , PHE A:78 , ASP A:80 , TYR A:126 , PRO A:162BINDING SITE FOR RESIDUE ACT A 2004
5AC5SOFTWAREGLU A:17 , SER A:68 , HOH A:3184 , HOH A:3295 , GLU B:1025 , ARG B:1028 , HOH B:3034BINDING SITE FOR RESIDUE ACT A 2005

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BGY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BGY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BGY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BGY)

(-) Exons   (0, 0)

(no "Exon" information available for 3BGY)

(-) 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:226
 aligned with MCE_MIMIV | Q5UQX1 from UniProtKB/Swiss-Prot  Length:1170

    Alignment length:226
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
           MCE_MIMIV     12 ITIFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKNRGSGKLIGIDNWAITIKSTEEIPLVAGKSKISKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD  237
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeeeeeeeeeeee.....eeeeeeeeeee................eeeeeeeeeeeeeee..eeeeeeeeeee....hhhhh..eeeeeeee....hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bgy A   12 ITIFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKNRGSGKLIGIDNWAITIKSTEEIPLVAGKSKISKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD  237
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with MCE_MIMIV | Q5UQX1 from UniProtKB/Swiss-Prot  Length:1170

    Alignment length:225
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232     
           MCE_MIMIV     13 TIFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKNRGSGKLIGIDNWAITIKSTEEIPLVAGKSKISKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD  237
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhh..eeeeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeeeeeeee.....eeeeee.hhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeee.hhhheeee.....eeeeeeeeeee...-............eeeeeeeeeeee.....eeeeeeeeeee....hhhhh..eeeeeeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3bgy B 1013 TIFSENEYNEIVEMLRDYSNGDNLEFEVSFKNINYPNFMRITEHYINITPENKIESNNYLDISLIFPDKNVYRVSLFNQEQIGEFITKFSKASSNDISRYIVSLDPSDDIEIVYKNRGSGKLIGIDNWAITIKSTEEIPLVAG-SKISKPKITGSERIMYRYKTRYSFTINKNSRIDITDVKSSPIIWKLMTVPSNYELELELINKIDINTLESELLNVFMIIQD 1237
                                  1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152  | | 1162      1172      1182      1192      1202      1212      1222      1232     
                                                                                                                                                                       1155 |                                                                                
                                                                                                                                                                         1157                                                                                

   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 3BGY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3BGY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BGY)

(-) 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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        MCE_MIMIV | Q5UQX12qy2 2qze

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2qy2 2qze