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(-) Description

Title :  COMPLEX STRUCTURE OF CCA-ADDING ENZYME WITH TRNAMINIDC AND CTP
 
Authors :  K. Tomita, R. Ishitani, S. Fukai, O. Nureki
Date :  08 Jun 06  (Deposition) - 14 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Rna Complex, Transferase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tomita, R. Ishitani, S. Fukai, O. Nureki
Complete Crystallographic Analysis Of The Dynamics Of Cca Sequence Addition
Nature V. 443 956 2006
PubMed-ID: 17051158  |  Reference-DOI: 10.1038/NATURE05204
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA (33-MER)
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - CCA-ADDING ENZYME
    Chains: A
    EC Number: 2.7.7.25, 2.7.7.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: TRNA NUCLEOTIDYLTRANSFERASE, TRNA ADENYLYL- /CYTIDYLYL- TRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, TRNA- NT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CTP1Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:299 , ARG A:302 , LYS A:303 , HOH A:623BINDING SITE FOR RESIDUE SO4 A 502
2AC2SOFTWAREGLU A:59 , ASP A:61 , CTP A:501BINDING SITE FOR RESIDUE MG A 503
3AC3SOFTWAREGLY A:46 , SER A:47 , ARG A:50 , ASP A:61 , THR A:130 , HIS A:133 , LYS A:152 , TYR A:161 , TYR A:173 , ARG A:224 , MG A:503 , HOH A:519 , HOH A:525 , HOH A:539 , HOH A:565 , HOH A:614 , HOH A:615 , A B:32 , C B:33BINDING SITE FOR RESIDUE CTP A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DR8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DR8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DR8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DR8)

(-) Exons   (0, 0)

(no "Exon" information available for 2DR8)

(-) Sequences/Alignments

Asymmetric/Biological 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:437
 aligned with CCA_ARCFU | O28126 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:437
                                    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       400       410       420       430       
            CCA_ARCFU     1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
               SCOP domains d2dr8a2 A:1-142 tRNA nucleotidyltransferase, N-terminal domain                                                                                d2dr8a1 A:143-257 tRNA nucleotidyltransferase, second domain                                                       d2dr8a3 A:258-437 tRNA nucleotidyltransferase, C-terminal domain                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.....eeeehhhhh........eeeeeeeee...hhhhhhhhhhhhhhhhh.eeee.......eeeee..eeeeeeeeee............hhhhhhhhhhh....hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhheeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhh.......eee..eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhh..hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dr8 A   1 MKVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    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       400       410       420       430       


Chain B from PDB  Type:RNA  Length:33
                                                                 
                 2dr8 B   1 GGCCCGGGGCGGUUCGAUUCCGCCCUGGGCCAC  33
                                    10        20        30
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DR8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DR8)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CCA_ARCFU | O28126)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0052929    ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity    Catalysis of the reaction: a tRNA with a 3' CC end + ATP = a tRNA with a 3' CCA end + diphosphate.
    GO:0052928    CTP:3'-cytidine-tRNA cytidylyltransferase activity    Catalysis of the reaction: a tRNA with a 3' cytidine + CTP = a tRNA with a 3' CC end + diphosphate.
    GO:0052927    CTP:tRNA cytidylyltransferase activity    Catalysis of the reaction: a tRNA precursor + CTP = a tRNA with a 3' cytidine end + diphosphate.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004810    tRNA adenylyltransferase activity    Catalysis of the reaction: ATP + tRNA(n) = diphosphate + tRNA(n+1).
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0016437    tRNA cytidylyltransferase activity    Catalysis of the reaction: CTP + tRNA(n) = diphosphate + tRNA(n+1).
    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:0031123    RNA 3'-end processing    Any process involved in forming the mature 3' end of an RNA molecule.
    GO:0042245    RNA repair    Any process that results in the repair of damaged RNA.
    GO:0001680    tRNA 3'-terminal CCA addition    Post-transcriptional addition of the terminal 3' CCA sequence to a tRNA which does not encode this sequence within the primary transcript. CCA addition proceeds by the sequential addition of CTP, CTP, and then ATP to the 3' end of the tRNA, yielding a diphosphate with each nucleotide addition.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CCA_ARCFU | O28126: 1r89 1r8a 1r8b 1r8c 1sz1 1tfw 1tfy 1uet 1ueu 1uev 2dr5 2dr7 2dr9 2dra 2drb 2dvi 2zh1 2zh2 2zh3 2zh4 2zh5 2zh6 2zh7 2zh8 2zh9 2zha 2zhb 3ouy 3ov7 3ova 3ovb 3ovs 4x4n 4x4o 4x4p 4x4q 4x4r 4x4s 4x4t 4x4u 4x4v

(-) Related Entries Specified in the PDB File

2dr5 2dr7 2dr9 2dra 2drb