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(-) Description

Title :  CRYSTAL STRUCTURE OF MAMMALIAN CAPPING ENZYME (MCE1) AND POL II CTD COMPLEX
 
Authors :  A. Ghosh, C. D. Lima
Date :  04 May 11  (Deposition) - 29 Jun 11  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  A,B,C  (1x)
Keywords :  Guanylyltransferase, Rna Polymerase Ii Ctd, Lysyl-N-Gmp, Nucleus, Mrna Capping, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ghosh, S. Shuman, C. D. Lima
Structural Insights To How Mammalian Capping Enzyme Reads The Ctd Code.
Mol. Cell V. 43 299 2011
PubMed-ID: 21683636  |  Reference-DOI: 10.1016/J.MOLCEL.2011.06.001

(-) Compounds

Molecule 1 - MRNA-CAPPING ENZYME
    ChainsA, B
    EC Number2.7.7.50
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidTOPO-ADAPTED PET28B-SMT3
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentGTASE DOMAIN (UNP RESIDUES 226-567)
    GeneCAP1A, MCE1, RNGTT
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainC57BL/6
    SynonymHCE, MCE1, POLYNUCLEOTIDE 5'-TRIPHOSPHATASE, TPASE, MRNA 5'- TRIPHOSPHATASE, MRNA GUANYLYLTRANSFERASE, GTP--RNA GUANYLYLTRANSFERASE, GTASE
 
Molecule 2 - RNA POLYMERASE II C-TERMINAL DOMAIN
    ChainsC
    EngineeredYES
    Other DetailsSYNTHETIC PHOSPHORYLATED PEPTIDE DERIVED FROM THE C- TERMINAL DOMAIN OF RNA POLYMERASE II
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) BC
Biological Unit 3 (1x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GUN2Ligand/IonGUANINE
2SEP4Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GUN1Ligand/IonGUANINE
2SEP-1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1GUN1Ligand/IonGUANINE
2SEP4Mod. Amino AcidPHOSPHOSERINE
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1GUN2Ligand/IonGUANINE
2SEP4Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:273 , ARG A:299 , ASP A:343 , GLY A:344 , GLU A:345 , ILE A:441 , GLN A:443BINDING SITE FOR RESIDUE GUN A 1
2AC2SOFTWAREHOH B:15 , PRO B:273 , LYS B:294 , ARG B:299 , ASP B:343 , GLY B:344 , GLU B:345 , TYR B:362BINDING SITE FOR RESIDUE GUN B 2

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gln A:247 -Pro A:248
2Gln B:247 -Pro B:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RTX)

(-) 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:262
 aligned with MCE1_MOUSE | O55236 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:343
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564   
           MCE1_MOUSE   225 RLKLGAIFLEGITVKGVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNIRLLEQKPYKVSWKADGTRYMMLIDGTNEVFMIDRDNSVFHVSNLEFPFRKDLRMHLSNTLLDGEMIIDKVNGQAVPRYLIYDIIKFNAQPVGDCDFNIRLQCIEREIISPRHEKMKTGLIDKTQEPFSVRPKQFFDINISRKLLEGNFAKEVSHEMDGLIFQPIGKYKPGRCDDILKWKPPSLNSVDFRLKITRMGGEGLLPQNVGLLYVGGYERPFAQIKVTKELKQYDNKIIECKFENNSWVFMRQRIDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDRCAA 567
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eee....hhhhhhhhhhhhhh.........eeeee...hhhhhhhhh.eeeeee...eeeeeee.....eeee.....eeee.....ee..eeeee...eeeeeeeeeee....eeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeee...ee..hhhhhh..----------.eeeeee......eeeeeeeee.......-----------------------------------------------------------------------hhhhhhhhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rtx A 225 SLKLGAIFLEGITVKGVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNIRLLEQKPYKVSWKADGTRYMMLIDGTNEVFMIDRDNSVFHVSNLEFPFRKDLRMHLSNTLLDGEMIIDKVNGQAVPRYLIYDIIKFNAQPVGDCDFNIRLQCIEREIISPRHEKMKTGLIDKTQEPFSVRPKQFFDINISRKLLEG----------DGLIFQPIGKYKPGRCDDILKWKPPSLNS-----------------------------------------------------------------------AYNTAMAVCNSISNPVTKEMLFEFIDRCAA 567
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424  |      -   |   444       454       464 |       -         -         -         -         -         -         -   |   544       554       564   
                                                                                                                                                                                                                                    427        438                         466                                                                     538                             

Chain B from PDB  Type:PROTEIN  Length:254
 aligned with MCE1_MOUSE | O55236 from UniProtKB/Swiss-Prot  Length:597

    Alignment length:343
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564   
           MCE1_MOUSE   225 RLKLGAIFLEGITVKGVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNIRLLEQKPYKVSWKADGTRYMMLIDGTNEVFMIDRDNSVFHVSNLEFPFRKDLRMHLSNTLLDGEMIIDKVNGQAVPRYLIYDIIKFNAQPVGDCDFNIRLQCIEREIISPRHEKMKTGLIDKTQEPFSVRPKQFFDINISRKLLEGNFAKEVSHEMDGLIFQPIGKYKPGRCDDILKWKPPSLNSVDFRLKITRMGGEGLLPQNVGLLYVGGYERPFAQIKVTKELKQYDNKIIECKFENNSWVFMRQRIDKSFPNAYNTAMAVCNSISNPVTKEMLFEFIDRCAA 567
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------mRNA_cap_enzyme-3rtxB01 B:272-460                                                                                                                                                            --mR                                                                                 NA_cap_C-3rtxB0------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------mRNA_cap_enzyme-3rtxB02 B:272-460                                                                                                                                                            --mR                                                                                 NA_cap_C-3rtxB0------- Pfam domains (2)
         Sec.struct. author ................eee....hhhhhhhhhhhhh..........eeeee...hhhhhhhh..eeeeee...eeeeeee.....eeee.....eeee.................eeeeeeeeeeee..eeeeeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh..eeee...ee..hhhhhhh..--------..eeeeee......eeeeeeeee.....---------------------------------------------------------------------------------hhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rtx B 225 SLKLGAIFLEGITVKGVTQVTTQPKLGEVQQKCHQFCGWEGSGFPGAQPVSMDKQNIRLLEQKPYKVSWKADGTRYMMLIDGTNEVFMIDRDNSVFHVSNLEFPFRKDLRMHLSNTLLDGEMIIDKVNGQAVPRYLIYDIIKFNAQPVGDCDFNIRLQCIEREIISPRHEKMKTGLIDKTQEPFSVRPKQFFDINISRKLLEGN--------MDGLIFQPIGKYKPGRCDDILKWKPPSL---------------------------------------------------------------------------------CNSISNPVTKEMLFEFIDRCAA 567
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   |     -  |    444       454       464         -         -         -         -         -         -         -         - |     554       564   
                                                                                                                                                                                                                                     428      437                        464                                                                               546                     

Chain C from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 3rtx C   2 sPSYsPTsPSYsP  14
                            |   |  |11 | 
                            2-SEP  |   | 
                                6-SEP  | 
                                   9-SEP 
                                      13-SEP

   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 3RTX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: OB (224)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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 1i9t

(-) Related Entries Specified in the PDB File

1i9s TRIPHOSPHATASE DOMAIN OF MOUSE MRNA CAPPING ENZYME
1i9t TRIPHOSPHATASE DOMAIN OF MOUSE MRNA CAPPING ENZYME