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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OXIDIZED RNA TRIPHOSPHATASE DOMAIN OF MOUSE MRNA CAPPING ENZYME
 
Authors :  A. Changela, C. K. Ho, A. Martins, S. Shuman, A. Mondragon
Date :  20 Mar 01  (Deposition) - 23 May 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (2x)
Keywords :  Rna Triphosphatase Domain, Mrna Capping Enzyme, Cysteine Sulfenic Acid, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Changela, C. K. Ho, A. Martins, S. Shuman, A. Mondragon
Structure And Mechanism Of The Rna Triphosphatase Component Of Mammalian Mrna Capping Enzyme.
Embo J. V. 20 2575 2001
PubMed-ID: 11350947  |  Reference-DOI: 10.1093/EMBOJ/20.10.2575

(-) Compounds

Molecule 1 - MRNA CAPPING ENZYME
    ChainsA
    EC Number3.1.3.33
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET16B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentTPASE DOMAIN (RESIDUES 1-210)
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMCE1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A
Biological Unit 3 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric Unit (5, 6)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4MG1Ligand/IonMAGNESIUM ION
5SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
1CAC1Ligand/IonCACODYLATE ION
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3IPA2Ligand/IonISOPROPYL ALCOHOL
4MG-1Ligand/IonMAGNESIUM ION
5SO41Ligand/IonSULFATE ION
Biological Unit 2 (4, 10)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3IPA4Ligand/IonISOPROPYL ALCOHOL
4MG-1Ligand/IonMAGNESIUM ION
5SO42Ligand/IonSULFATE ION
Biological Unit 3 (4, 10)
No.NameCountTypeFull Name
1CAC2Ligand/IonCACODYLATE ION
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3IPA4Ligand/IonISOPROPYL ALCOHOL
4MG-1Ligand/IonMAGNESIUM ION
5SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:32 , PRO A:33 , ARG A:34 , HOH A:615 , HOH A:656 , HOH A:700 , HOH A:792 , HOH A:811 , HOH A:813 , HOH A:814 , HOH A:816BINDING SITE FOR RESIDUE SO4 A 300
2AC2SOFTWAREARG A:9 , TYR A:165 , CYS A:193BINDING SITE FOR RESIDUE CAC A 400
3AC3SOFTWAREHOH A:811 , HOH A:812 , HOH A:813 , HOH A:814 , HOH A:815 , HOH A:816BINDING SITE FOR RESIDUE MG A 500
4AC4SOFTWAREARG A:15 , ARG A:16 , IPA A:601 , HOH A:760 , HOH A:783BINDING SITE FOR RESIDUE IPA A 600
5AC5SOFTWAREARG A:16 , TYR A:53 , IPA A:600BINDING SITE FOR RESIDUE IPA A 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1I9T)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:117 -Pro A:118
2Pro A:161 -Pro A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1I9T)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.MCE1_MOUSE104-171  1A:104-171
2TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.MCE1_MOUSE124-134  1A:124-134
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.MCE1_MOUSE104-171  1A:104-171
2TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.MCE1_MOUSE124-134  1A:124-134
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.MCE1_MOUSE104-171  2A:104-171
2TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.MCE1_MOUSE124-134  2A:124-134
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.MCE1_MOUSE104-171  2A:104-171
2TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.MCE1_MOUSE124-134  2A:124-134

(-) Exons   (0, 0)

(no "Exon" information available for 1I9T)

(-) 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:190
 aligned with MCE1_MOUSE | O55236 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:190
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
           MCE1_MOUSE     5 KIPPRWLNCPRRGQPVAGRFLPLKTMLGPRYDSQVAEENRFHPSMLSNYLKSLKVKMSLLVDLTNTSRFYDRNDIEKEGIKYIKLQCKGHGECPTTENTETFIRLCERFNERSPPELIGVHCTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRYGDIEEAPPPPVLPDWCF 194
               SCOP domains d1i9ta_ A: mRNA capping enzyme, triphosphatase domain                                                                                                                                          SCOP domains
               CATH domains 1i9tA00 A:5-194 Protein tyrosine phosphatase superfamily                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eee.....hhhhhhhhhhhhh.hhhhhhhhhhhh...eeeeee........hhhhhhh...eeee..........hhhhhhhhhhhhh.........eeeee....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh......hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:104-171 UniProt: 104-171                  ----------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i9t A   5 KIPPRWLNCPRRGQPVAGRFLPLKTMLGPRYDSQVAEENRFHPSMLSNYLKSLKVKMSLLVDLTNTSRFYDRNDIEKEGIKYIKLQCKGHGECPTTENTETFIRLCERFNERSPPELIGVHcTHGFNRTGFLICAFLVEKMDWSIEAAVATFAQARPPGIYKGDYLKELFRRYGDIEEAPPPPVLPDWCF 194
                                    14        24        34        44        54        64        74        84        94       104       114       124 |     134       144       154       164       174       184       194
                                                                                                                                                   126-CSO                                                                

   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 Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1I9T)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A   (MCE1_MOUSE | O55236)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0008192    RNA guanylyltransferase activity    Catalysis of the posttranscriptional addition of a guanyl residue to the 5' end of an RNA molecule.
    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: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: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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0004651    polynucleotide 5'-phosphatase activity    Catalysis of the reaction: 5'-phosphopolynucleotide + H2O = polynucleotide + phosphate.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0008138    protein tyrosine/serine/threonine phosphatase activity    Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + 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.
    GO:0050355    triphosphatase activity    Catalysis of the reaction: H(2)O + triphosphate = diphosphate + phosphate.
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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a 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:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0098507    polynucleotide 5' dephosphorylation    The process of removing one or more phosphate groups from the 5' end of a polynucleotide.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
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
        MCE1_MOUSE | O552361i9s 3rtx

(-) Related Entries Specified in the PDB File

1i9s NATIVE MOUSE RNA TRIPHOSPHATASE DOMAIN