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(-) Description

Title :  DIVERGENT EVOLUTIONS OF TRINUCLEOTIDE POLYMERIZATION REVEALED BY AN ARCHAEAL CCA-ADDING ENZYME STRUCTURE
 
Authors :  O. Nureki, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  21 May 03  (Deposition) - 02 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Okabe, K. Tomita, R. Ishitani, R. Ishii, N. Takeuchi, F. Arisaka, O. Nureki, S. Yokoyama
Divergent Evolutions Of Trinucleotide Polymerization Revealed By An Archaeal Cca-Adding Enzyme Structure.
Embo J. V. 22 5918 2003
PubMed-ID: 14592988  |  Reference-DOI: 10.1093/EMBOJ/CDG563
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA NUCLEOTIDYLTRANSFERASE
    Chains: A
    EC Number: 2.7.7.25
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PET22B
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CA3Ligand/IonCALCIUM ION
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:59 , ASP A:61 , ASP A:110 , HOH A:687BINDING SITE FOR RESIDUE MG A 601
2AC2SOFTWARELYS A:166 , CA A:604BINDING SITE FOR RESIDUE CA A 602
3AC3SOFTWARETHR A:383 , GLU A:387BINDING SITE FOR RESIDUE CA A 603
4AC4SOFTWARECA A:602 , HOH A:614 , HOH A:675BINDING SITE FOR RESIDUE CA A 604
5AC5SOFTWAREVAL A:45 , GLY A:46 , SER A:47 , ARG A:50 , THR A:52 , TRP A:53 , LEU A:54 , GLU A:59 , ASP A:61 , THR A:130 , HIS A:133 , LYS A:152 , TYR A:161 , GLY A:172 , TYR A:173 , GLU A:176 , HOH A:686BINDING SITE FOR RESIDUE ATP A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UEV)

(-) 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:431
 aligned with CCA_ARCFU | O28126 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:436
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431      
            CCA_ARCFU     2 KVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSYEIRYAEHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
               SCOP domains d1ueva2 A:2-142 tRNA nucleotidyltransferase, N-terminal domain                                                                               d1ueva1 A:143-257 tRNA nucleotidyltransferase, second domain                                                       d1ueva3 A:258-437 tRNA nucleotidyltransferase, C-terminal domain                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------NTP_transf_2-1uevA01 A:25-133                                                                                ------------tRNA_NucTransf2-1uevA02 A:146-256                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eee...............eeeeee......hhhhhhhhhhhh.eeeee.-----...eeeeee..eeeeeeee..............hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.....eeee.hhheeee....eeee..eeeee.....hhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee...eeeeeeee.......eeeeeeee..hhhhhhhhhhh......ee...eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhhhh.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uev A   2 KVEEILEKALELVIPDEEEVRKGREAEEELRRRLDELGVEYVFVGSYARNTWLKGSLEIDVFLLFPEEFSKEELRERGLEIGKAVLDSY-----EHPYVHGVVKGVEVDVVPCYKLKEPKNIKSAVDRTPFHHKWLEGRIKGKENEVRLLKGFLKANGIYGAEYKVRGFSGYLCELLIVFYGSFLETVKNARRWTRRTVIDVAKGEVRKGEEFFVVDPVDEKRNVAANLSLDNLARFVHLCREFMEAPSLGFFKPKHPLEIEPERLRKIVEERGTAVFAVKFRKPDIVDDNLYPQLERASRKIFEFLERENFMPLRSAFKASEEFCYLLFECQIKEISRVFRRMGPQFEDERNVKKFLSRNRAFRPFIENGRWWAFEMRKFTTPEEGVRSYASTHWHTLGKNVGESIREYFEIISGEKLFKEPVTAELCEMMGVKD 437
                                    11        21        31        41        51        61        71        81        |-    |  101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431      
                                                                                                                   90    96
   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 1UEV)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: NTP_transf (45)
(-)
Clan: no clan defined [family: tRNA_NucTransf2] (21)

(-) 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 2dr5 2dr7 2dr8 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

1uet THE SAME PROTEIN WITH ACETATE ION
1ueu THE SAME PROTEIN WITH CYTIDINE-5'-TRIPHOSPHATE RELATED ID: TRT001000261.2 RELATED DB: TARGETDB