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(-) Description

Title :  STRUCTURE OF TWO DIFFERENT CONFORMATIONS OF MRNA CAPPING ENZYME IN COMPLEX WITH GTP
 
Authors :  K. Hakansson, A. J. Doherty, D. B. Wigley
Date :  20 Apr 97  (Deposition) - 07 Jul 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Biol. Unit 4:  A,B  (1x)
Biol. Unit 5:  A  (2x)
Keywords :  Mrna, Capping Enzyme, Nucleotidyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Hakansson, A. J. Doherty, S. Shuman, D. B. Wigley
X-Ray Crystallography Reveals A Large Conformational Change During Guanyl Transfer By Mrna Capping Enzymes.
Cell(Cambridge, Mass. ) V. 89 545 1997
PubMed-ID: 9160746  |  Reference-DOI: 10.1016/S0092-8674(00)80236-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MRNA CAPPING ENZYME
    Chains: A, B
    EC Number: 2.7.7.50
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PARAMECIUM BURSARIA CHLORELLA VIRUS 1
    Organism Taxid: 10506
    Synonym: RNA GUANYLYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB
Biological Unit 4 (1x): AB
Biological Unit 5 (2x): A 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GTP1Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1GTP4Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1GTP2Ligand/IonGUANOSINE-5'-TRIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:59 , PRO A:61 , LYS A:82 , THR A:83 , ARG A:87 , ARG A:106 , GLU A:131 , PHE A:146 , LYS A:188 , TRP A:190 , ILE A:216 , LEU A:232 , LYS A:234 , HOH A:972 , HOH A:1043 , HOH A:1061 , HOH A:1062BINDING SITE FOR RESIDUE GTP A 899
2AC2SOFTWAREPRO B:59 , LYS B:82 , THR B:83 , ARG B:87 , ARG B:106 , GLU B:131 , PHE B:146 , LYS B:188 , TRP B:190 , ILE B:216 , ARG B:228 , LYS B:234 , LYS B:236 , ASP B:244 , ARG B:295 , LYS B:298 , ASN B:302 , HOH B:1062 , HOH B:1105 , HOH B:1148 , HOH B:1149 , HOH B:1150 , HOH B:1155 , HOH B:1173 , HOH B:1175BINDING SITE FOR RESIDUE GTP B 999
3GPAUNKNOWNLYS A:82ACTIVE SITE LYSINE.
4GPBUNKNOWNLYS B:82ACTIVE SITE LYSINE.

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1CKM)

(-) 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:317
 aligned with MCE_PBCV1 | Q84424 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:317
                                    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       
            MCE_PBCV1    11 NITTERAVLTLNGLQIKLHKVVGESRDDIVAKMKDLAMDDHKFPRLPGPNPVSIERKDFEKLKQNKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTVYLLPFKNIPRVLFQGSIFDGELCVDIVEKKFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAILRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSVDEPVIYGRNFNLFKLKPGTHHTIDFIIMSEDGTIGIFDPNLRKNVPVGKLDGYYNKGSIVECGFADGTWKYIQGRSDKNQANDRLTYEKTLLNIEENITIDELLDLF 327
               SCOP domains d1ckma2 A:11-238 RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain                                                                                                                                                   d1ckma1 A:239-327 RNA guanylyltransferase (mRNA capping enzyme)                           SCOP domains
               CATH domains 1ckmA01 A:11-59,A:84-189                         ------------------------1ckmA01 A:11-59,A:84-189 DNA ligase/mRNA capping enzyme                                                   1ckmA03 A:190-235,A:319-326                   1ckmA02 A:236-318 Nucleic acid-binding proteins                                    1ckmA03 - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeee.hhhhhhhhhhhhhh...................hhhhhhhhh..eeeee....eeeeeeeeee..eeeeeee.....eee.........hhh.eeeeeeeeee....eeeeee.eeee..........hhhhhhhhhhhhhh.........eeee........hhhhhhhhhhhhhh.....eeeee............eeee.......eeee........eeee....eeee............eeeeeee..eeeeeee.........hhhhhhhhhhhhh...hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ckm A  11 NITTERAVLTLNGLQIKLHKVVGESRDDIVAKMKDLAMDDHKFPRLPGPNPVSIERKDFEKLKQNKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTVYLLPFKNIPRVLFQGSIFDGELCVDIVEKKFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAILRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSVDEPVIYGRNFNLFKLKPGTHHTIDFIIMSEDGTIGIFDPNLRKNVPVGKLDGYYNKGSIVECGFADGTWKYIQGRSDKNQANDRLTYEKTLLNIEENITIDELLDLF 327
                                    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       


Chain B from PDB  Type:PROTEIN  Length:317
 aligned with MCE_PBCV1 | Q84424 from UniProtKB/Swiss-Prot  Length:330

    Alignment length:317
                                    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       
            MCE_PBCV1    11 NITTERAVLTLNGLQIKLHKVVGESRDDIVAKMKDLAMDDHKFPRLPGPNPVSIERKDFEKLKQNKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTVYLLPFKNIPRVLFQGSIFDGELCVDIVEKKFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAILRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSVDEPVIYGRNFNLFKLKPGTHHTIDFIIMSEDGTIGIFDPNLRKNVPVGKLDGYYNKGSIVECGFADGTWKYIQGRSDKNQANDRLTYEKTLLNIEENITIDELLDLF 327
               SCOP domains d1ckmb2 B:11-238 RNA guanylyltransferase (mRNA capping enzyme), N-terminal domain                                                                                                                                                   d1ckmb1 B:239-327 RNA guanylyltransferase (mRNA capping enzyme)                           SCOP domains
               CATH domains 1ckmB01 B:11-59,B:84-189                         ------------------------1ckmB01 B:11-59,B:84-189 DNA ligase/mRNA capping enzyme                                                   1ckmB03 B:190-235,B:319-326                   1ckmB02 B:236-318 Nucleic acid-binding proteins                                    1ckmB03 - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeee.hhhhhhhhhhhhhhh..................hhhhhhhhh..eeeee....eeeeeeeeee..eeeeeee.....eee.......hhhhh.eeeeeeeeee....eeeeee.eeee..........hhhhhhhhhhhh...........eeee........hhhhhhhhhhhhh......eeeee.............eee......eeeeeeee...eeeeeehhh.eeeeeee.........eeeeeee..eeeeeee.........hhhhhhhhhhhh....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ckm B  11 NITTERAVLTLNGLQIKLHKVVGESRDDIVAKMKDLAMDDHKFPRLPGPNPVSIERKDFEKLKQNKYVVSEKTDGIRFMMFFTRVFGFKVCTIIDRAMTVYLLPFKNIPRVLFQGSIFDGELCVDIVEKKFAFVLFDAVVVSGVTVSQMDLASRFFAMKRSLKEFKNVPEDPAILRYKEWIPLEHPTIIKDHLKKANAIYHTDGLIIMSVDEPVIYGRNFNLFKLKPGTHHTIDFIIMSEDGTIGIFDPNLRKNVPVGKLDGYYNKGSIVECGFADGTWKYIQGRSDKNQANDRLTYEKTLLNIEENITIDELLDLF 327
                                    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
   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  (3, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MCE_PBCV1 | Q84424)
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.

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 Related Entries

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        MCE_PBCV1 | Q84424: 1ckn 1cko

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