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(-) Description

Title :  STRUCTURE OF AN MRNA CAPPING ENZYME BOUND TO THE PHOSPHORYLATED CARBOXYL-TERMINAL DOMAIN OF RNA POLYMERASE II
 
Authors :  C. Fabrega, V. Shen, S. Shuman, C. D. Lima
Date :  11 Apr 03  (Deposition) - 15 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Guanylyltransferase, Candida Albicans, Rna Polymerase Ii, Transcription, Capping, Ctd, Mrna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Fabrega, V. Shen, S. Shuman, C. D. Lima
Structure Of An Mrna Capping Enzyme Bound To The Phosphorylated Carboxy-Terminal Domain Of Rna Polymerase Ii.
Mol. Cell V. 11 1549 2003
PubMed-ID: 12820968  |  Reference-DOI: 10.1016/S1097-2765(03)00187-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MRNA CAPPING ENZYME ALPHA SUBUNIT
    Chains: A, B
    EC Number: 2.7.7.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSMT3
    Expression System Taxid: 562
    Expression System Variant: B834 (DE3)
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-395 OD SWS P78587
    Gene: CGT1
    Mutation: YES
    Organism Scientific: CANDIDA ALBICANS
    Organism Taxid: 5476
    Other Details: MODIFIED PET15B (N-TERMINAL SUMO FUSION)
    Synonym: MRNA GUANYLYLTRANSFERASE
 
Molecule 2 - PHOSPHORYLATED PEPTIDE FROM C-TERMINAL OF RNA POLYMERASE II
    Chains: C, D
    Engineered: YES
    Other Details: NATURALLY OCCURING REPETITIVE YSPTSPS SEQUENCE
    Synonym: PHOSPHORYLATED CTD PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 24)

Asymmetric Unit (5, 24)
No.NameCountTypeFull Name
1G1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MSE14Mod. Amino AcidSELENOMETHIONINE
4PO43Ligand/IonPHOSPHATE ION
5SEP5Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1G-1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2GTP-1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MSE7Mod. Amino AcidSELENOMETHIONINE
4PO43Ligand/IonPHOSPHATE ION
5SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (3, 11)
No.NameCountTypeFull Name
1G-1Ligand/IonGUANOSINE-5'-MONOPHOSPHATE
2GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
3MSE7Mod. Amino AcidSELENOMETHIONINE
4PO4-1Ligand/IonPHOSPHATE ION
5SEP3Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:44 , ARG A:92 , LYS A:241 , G A:1167 , HOH A:7097BINDING SITE FOR RESIDUE PO4 A 7001
2AC2SOFTWARELYS A:23BINDING SITE FOR RESIDUE PO4 A 7002
3AC3SOFTWAREARG A:26BINDING SITE FOR RESIDUE PO4 A 7005
4AC4SOFTWAREGLN A:44 , PRO A:45 , CYS A:65 , LYS A:67 , THR A:68 , GLU A:126 , PHE A:144 , LYS A:197 , ILE A:223 , LEU A:239 , PO4 A:7001 , HOH A:7092 , HOH A:7135BINDING SITE FOR RESIDUE G A 1167
5AC5SOFTWAREGLN B:44 , PRO B:45 , LYS B:67 , ARG B:72 , GLU B:126 , PHE B:144 , LYS B:197 , ILE B:223 , LEU B:239 , LYS B:241 , LYS B:243 , HOH B:5051 , HOH B:5132 , HOH B:5151BINDING SITE FOR RESIDUE GTP B 5001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P16)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1P16)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P16)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P16)

(-) Exons   (0, 0)

(no "Exon" information available for 1P16)

(-) 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:390
 aligned with MCE1_CANAX | P78587 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:390
                                    10        20        30        40        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       300       310       320       330       340       350       360       370       380       390
           MCE1_CANAX     1 MIQLEEREIPVIPGNKLDEEETKELRLMVAELLGRRNTGFPGSQPVSFERRHLEETLMQKDYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYYFIPNIHFPLSVNETREKPTYHHGTLLDGELVLENRNVSEPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVMKPFDNFKKHNPDIVNSPEFPFKVGFKTMLTSYHADDVLSKMDKLFHASDGLIYTCAETPYVFGTDQTLLKWKPAEENTVDFQLEFVFNEVQDPDLDERDPTSTYLDYDAKPNLIKLRVWQGSNVHTDFAKLDLSDDDWERLKALEQPLQGRIAECRQSTTKKGYWEMLRFRNDKSNGNHISVVEKILVSIKDGVKEKEVIEWCPKISRAWKKRENDRRQ 390
               SCOP domains d1p16a2 A:1-245 mRNA capping enzyme alpha subunit                                                                                                                                                                                                    d1p16a1 A:246-390 mRNA capping enzyme alpha subunit                                                                                               SCOP domains
               CATH domains -1p16A----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1p16A01 A:2-6,A:245-390 Nucleic acid-binding proteins                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..............ee.hhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhh.eeeeeee..eeeeeeeeee...eeeeeeee....eee......................eeeeeeeeee.......eeeeeeeeeeee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...ee...hhhhhhhhhhh...eeeeeeee.......eeeeeeeee.hhhhh.eeeeeeee.eeee...........eeee......eeeeeee.....eeeeeee..hhhhhhhhhhh.......eeeeee......eeeeeee........hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1p16 A   1 mVQLEEREIPVIPGNKLDEEETKELRLmVAELLGRRNTGFPGSQPVSFERRHLEETLmQKDYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYYFIPNIHFPLSVNETREKPTYHHGTLLDGELVLENRNVSEPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVmKPFDNFKKHNPDIVNSPEFPFKVGFKTmLTSYHADDVLSKmDKLFHASDGLIYTCAETPYVFGTDQTLLKWKPAEENTVDFQLEFVFNEVQDPDLDERDPTSTYLDYDAKPNLIKLRVWQGSNVHTDFAKLDLSDDDWERLKALEQPLQGRIAECRQSTTKKGYWEmLRFRNDKSNGNHISVVEKILVSIKDGVKEKEVIEWCPKISRAWKKRENDRRQ 390
                            |       10        20       |30        40        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       300       310       320       330       340       350       360       370       380       390
                            |                         28-MSE                        58-MSE                                                                                                          171-MSE                     199-MSE      212-MSE                                                                                                                       338-MSE                                                
                            1-MSE                                                                                                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:377
 aligned with MCE1_CANAX | P78587 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:389
                                    10        20        30        40        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       300       310       320       330       340       350       360       370       380         
           MCE1_CANAX     1 MIQLEEREIPVIPGNKLDEEETKELRLMVAELLGRRNTGFPGSQPVSFERRHLEETLMQKDYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYYFIPNIHFPLSVNETREKPTYHHGTLLDGELVLENRNVSEPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVMKPFDNFKKHNPDIVNSPEFPFKVGFKTMLTSYHADDVLSKMDKLFHASDGLIYTCAETPYVFGTDQTLLKWKPAEENTVDFQLEFVFNEVQDPDLDERDPTSTYLDYDAKPNLIKLRVWQGSNVHTDFAKLDLSDDDWERLKALEQPLQGRIAECRQSTTKKGYWEMLRFRNDKSNGNHISVVEKILVSIKDGVKEKEVIEWCPKISRAWKKRENDRR 389
               SCOP domains d1p16b2 B:1-245 mRNA capping enzyme alpha subunit                                                                                                                                                                                                    d1p16b1 B:246-389             mRNA capping enzyme alpha subunit                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1p16B02 B:245-389             Nucleic acid-binding proteins                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhhhhhh.........eeeee.hhhhhhhhhhhh.eeeeee...eeeeeeeeee...eeeeeeee....eee......................eeeeeeeeee.......eeeeeeeeeeee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee...ee..hhhhhhhhhhhh.....eeeeee.......eeeeeeeee.hhhhh.eeeeeee......------------..........eeeeee.....eeeeeee..hhhhhhhhhhh.......eeeeee......eeeeeeee.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p16 B   1 mVQLEEREIPVIPGNKLDEEETKELRLmVAELLGRRNTGFPGSQPVSFERRHLEETLmQKDYFVCEKTDGLRCLLFLINDPDKGEGVFLVTRENDYYFIPNIHFPLSVNETREKPTYHHGTLLDGELVLENRNVSEPVLRYVIFDALAIHGKCIIDRPLPKRLGYITENVmKPFDNFKKHNPDIVNSPEFPFKVGFKTmLTSYHADDVLSKmDKLFHASDGLIYTCAETPYVFGTDQTLLKWKPAEENTVDFQLEFVFNEVQ------------YLDYDAKPNLIKLRVWQGSNVHTDFAKLDLSDDDWERLKALEQPLQGRIAECRQSTTKKGYWEmLRFRNDKSNGNHISVVEKILVSIKDGVKEKEVIEWCPKISRAWKKRENDRR 389
                            |       10        20       |30        40        50       |60        70        80        90       100       110       120       130       140       150       160       170|      180       190       200       210 |     220       230       240       250       260 |       -    |  280       290       300       310       320       330       340       350       360       370       380         
                            1-MSE                     28-MSE                        58-MSE                                                                                                          171-MSE                     199-MSE      212-MSE                                           262          275                                                            338-MSE                                               


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               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
                 1p16 C 104 TsPSYSPTs 112
                             |      |
                           105-SEP  |
                                  112-SEP


Chain D from PDB  Type:PROTEIN  Length:17
                                                 
               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
                 1p16 D 104 TsPSYSPTsPSYSPTsP 120
                             |     113     | 
                             |      |      | 
                           105-SEP  |      | 
                                  112-SEP  | 
                                         119-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  (2, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1P16)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MCE1_CANAX | P78587)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    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: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: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.
cellular component
    GO:0031533    mRNA cap methyltransferase complex    A protein complex that consists of an RNA 5' triphosphatase and a guanyl transferase (Cet1p and Ceg1p in S. cerevisiae; Pct1 and Ceg1 in S. pombe) and is involved in mRNA capping.
    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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