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(-) Description

Title :  THE COMPLEX STRUCTURE OF CCA-ADDING ENZYME WITH ATP
 
Authors :  Y. Toh, K. Tomita
Date :  16 Apr 09  (Deposition) - 13 Oct 09  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Transferase/Rna, Nucleotide-Binding, Nucleotidyltransferase, Rna- Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Toh, D. Takeshita, T. Numata, S. Fukai, O. Nureki, K. Tomita
Mechanism For The Definition Of Elongation And Termination By The Class Ii Cca-Adding Enzyme
Embo J. V. 28 3353 2009
PubMed-ID: 19745807  |  Reference-DOI: 10.1038/EMBOJ.2009.260

(-) Compounds

Molecule 1 - TRNA NUCLEOTIDYL TRANSFERASE-RELATED PROTEIN
    Chains: A, B
    EC Number: 2.7.7.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 437-863
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: TRNA NUCLEOTIDYLTRANSFERASE, TRNA ADENYL-/CYTIDYL- TRANSFERASE, TRNA CCA-PYROPHOSPHORYLASE, TRNA-NT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:41 , GLY A:42 , ARG A:45 , ARG A:129 , ASP A:130 , ASN A:134 , ASP A:174 , THR A:176 , ARG A:177 , ARG A:180 , ARG A:183 , PHE A:184 , ARG A:187 , LYS A:223 , HOH A:461 , HOH A:462BINDING SITE FOR RESIDUE ATP A 501
2AC2SOFTWAREGLY B:42 , ARG B:45 , ARG B:129 , ASP B:130 , ASN B:134 , ASP B:174 , ARG B:177 , ARG B:180 , ARG B:183 , ARG B:187BINDING SITE FOR RESIDUE ATP B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H39)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H39)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H39)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3H39)

(-) Exons   (0, 0)

(no "Exon" information available for 3H39)

(-) 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:415
 aligned with Q9WZH4_THEMA | Q9WZH4 from UniProtKB/TrEMBL  Length:863

    Alignment length:425
                                   445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855     
         Q9WZH4_THEMA   436 GQIFRDVSKLLVERVDPKILNLFRLLGKFGDEVNMPVYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFMTASLFLKGGLRIDIATARLEYYESPAKLPDVEMSTIKKDLYRRDFTINAMAIKLNPKDFGLLIDFFGGYRDLKEGVIRVLHTLSFVDDPTRILRAIRFEQRFDFRIEETTERLLKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRMAQFDVIKHLFPKTYYTPSMDEKMENLFRNIPWVEENFGEVDRFYAVLHVFLEFYDDESWKEVRDRYSLRRNLINEIRHVEKSAPALLEMLSERVPASFVYPLVKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEKINGEYLIRKGITSGKIIGEVLEKILMKKLDGDTRDEEEILEEVLASLE 860
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh....eeeeee..hhhhhhhhhhh....eeeee....eeeeee...eeeeeee...----------.....hhhhhhhh..hhhhh.eee.hhhhh.eee...hhhhhhhh.ee.....hhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhh.......hhhhhhh..hhhhhhhhhhhhhhhhhhh....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h39 A   1 MQIFRDVSKLLVERVDPKILNLFRLLGKFGDEVNMPVYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFMTASLFLKGGLRIDIATARL----------DVEMSTIKKDLYRRDFTINAMAIKLNPKDFGLLIDFFGGYRDLKEGVIRVLHTLSFVDDPTRILRAIRFEQRFDFRIEETTERLLKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRMAQFDVIKHLFPKTYYTPSMDEKMENLFRNIPWVEENFGEVDRFYAVLHVFLEFYDDESWKEVRDRYSLRRNLINEIRHVEKSAPALLEMLSERVPASFVYPLVKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEKINGEYLIRKGITSGKIIGEVLEKILMKKLDGDTRDEEEILEEVLASLE 425
                                    10        20        30        40        50        60        70        80        90       100    |    -     | 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     
                                                                                                                                  105        116                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:420
 aligned with Q9WZH4_THEMA | Q9WZH4 from UniProtKB/TrEMBL  Length:863

    Alignment length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     863    
                                   445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       | -  
         Q9WZH4_THEMA   436 GQIFRDVSKLLVERVDPKILNLFRLLGKFGDEVNMPVYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFMTASLFLKGGLRIDIATARLEYYESPAKLPDVEMSTIKKDLYRRDFTINAMAIKLNPKDFGLLIDFFGGYRDLKEGVIRVLHTLSFVDDPTRILRAIRFEQRFDFRIEETTERLLKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRMAQFDVIKHLFPKTYYTPSMDEKMENLFRNIPWVEENFGEVDRFYAVLHVFLEFYDDESWKEVRDRYSLRRNLINEIRHVEKSAPALLEMLSERVPASFVYPLVKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEKINGEYLIRKGITSGKIIGEVLEKILMKKLDGDTRDEEEILEEVLASLETEG----   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeehhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhh.....eeeee..hhhhhhhhhhh....eeeee....eeeeee...eeeeeee...------------...hhhhhhhh..hhhhh.eee.hhhhh.eee...hhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhh......hhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh......hhhhhhhhhhhhhh......hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3h39 B   1 MQIFRDVSKLLVERVDPKILNLFRLLGKFGDEVNMPVYVVGGFVRDLLLGIKNLDIDIVVEGNALEFAEYAKRFLPGKLVKHDKFMTASLFLKGGLRIDIATARL------------EMSTIKKDLYRRDFTINAMAIKLNPKDFGLLIDFFGGYRDLKEGVIRVLHTLSFVDDPTRILRAIRFEQRFDFRIEETTERLLKQAVEEGYLERTTGPRLRQELEKILEEKNPLKSIRRMAQFDVIKHLFPKTYYTPSMDEKMENLFRNIPWVEENFGEVDRFYAVLHVFLEFYDDESWKEVRDRYSLRRNLINEIRHVEKSAPALLEMLSERVPASFVYPLVKGVSNETICHFLAYLSGEKEGLFKSYLLKIKNTKLEKINGEYLIRKGITSGKIIGEVLEKILMKKLDGDTRDEEEILEEVLASLETEGKLAA 432
                                    10        20        30        40        50        60        70        80        90       100    |    -       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  
                                                                                                                                  105          118
   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 3H39)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3H39)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H39)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9WZH4_THEMA | Q9WZH4)
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: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:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    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.

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  3h39
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 Related Entries

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

UniProtKB/TrEMBL
        Q9WZH4_THEMA | Q9WZH4: 3h37 3h38 3h3a 5hc9

(-) Related Entries Specified in the PDB File

3h37 3h38 3h3a