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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CCA-ADDING ENZYME
 
Authors :  M. A. Augustin, A. S. Reichert, H. Betat, R. Huber, M. Moerl, C. Steegborn
Date :  24 Mar 03  (Deposition) - 06 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trna, Polymerase, Nucleotidyltransferase, Translation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Augustin, A. S. Reichert, H. Betat, R. Huber, M. Moerl, C. Steegborn
Crystal Structure Of The Human Cca-Adding Enzyme: Insights Into Template-Independent Polymerization
J. Mol. Biol. V. 328 985 2003
PubMed-ID: 12729736  |  Reference-DOI: 10.1016/S0022-2836(03)00381-4
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRNA CCA-ADDING ENZYME
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30EK-LIC
    Expression System StrainBL21(DE3)RP
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneHMTCCA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCCA-ADDING ENZYME;
TRNA-NUCLEOTIDYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1OU5)

(-) Sites  (0, 0)

(no "Site" information available for 1OU5)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:344 -B:344

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1OU5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 12)

Asymmetric/Biological Unit (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_072421T154ITRNT1_HUMANDisease (SIFD)606231290A/BT125I
2UniProtVAR_072422M158VTRNT1_HUMANDisease (SIFD)771781629A/BM129V
3UniProtVAR_072423L166STRNT1_HUMANDisease (SIFD)606231289A/BL137S
4UniProtVAR_072424R190ITRNT1_HUMANDisease (SIFD)606231287A/BR161I
5UniProtVAR_072425I223TTRNT1_HUMANDisease (SIFD)370011798A/BI194T
6UniProtVAR_072426I326TTRNT1_HUMANDisease (SIFD)  ---A/BI297T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OU5)

(-) Exons   (7, 14)

Asymmetric/Biological Unit (7, 14)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002516071aENSE00001416815chr3:3168600-316867475TRNT1_HUMAN-00--
1.2aENST000002516072aENSE00002201846chr3:3170698-3170872175TRNT1_HUMAN1-50502A:-1-21
B:-1-21
23
23
1.6cENST000002516076cENSE00000997141chr3:3178944-3179137194TRNT1_HUMAN50-114652A:21-85
B:21-85
65
65
1.7aENST000002516077aENSE00000997135chr3:3182194-3182332139TRNT1_HUMAN115-161472A:86-132 (gaps)
B:86-132 (gaps)
47
47
1.8ENST000002516078ENSE00000997136chr3:3186268-3186394127TRNT1_HUMAN161-203432A:132-174
B:132-174
43
43
1.9bENST000002516079bENSE00001387479chr3:3188114-3188307194TRNT1_HUMAN203-268662A:174-239
B:174-239
66
66
1.10ENST0000025160710ENSE00000851845chr3:3189134-3189387254TRNT1_HUMAN268-352852A:239-323
B:239-323
85
85
1.11bENST0000025160711bENSE00001528667chr3:3189590-31907071118TRNT1_HUMAN353-434822A:324-354
B:324-354
31
31

(-) 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:344
 aligned with TRNT1_HUMAN | Q96Q11 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:356
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377      
          TRNT1_HUMAN    28 FTMKLQSPEFQSLFTEGLKSLTELFVKENHELRIAGGAVRDLLNGVKPQDIDFATTATPTQMKEMFQSAGIRMINNRGEKHGTITARLHEENFEITTLRIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVDKPGDHDPETLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSI 383
               SCOP domains d1ou5a2 A:-1-150 tRNA CCA-adding enzyme, head domain                                                                                                    d1ou5a1 A:151-354 tRNA CCA-adding enzyme, C-terminal domains                                                                                                                                                 SCOP domains
               CATH domains 1ou5A01 A:-1-150 Beta Polymerase, domain 2                                                                                                              1ou5A02 A:151-354 cca-adding enzyme, domain 2                                                                                                                                                                CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh..hhhhhhhhhhhh...eeee...hhhhhhh......eeee..hhhhhhhhhh................eee......eeeee...------------.......hhhhh.hhhhh.ee.....ee...hhhhhh...................hhhhhhhhhhhhh.......hhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhh...hhhhhhhhhh...............hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------I---V-------S-----------------------I--------------------------------T------------------------------------------------------------------------------------------------------T--------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:-1-21----------------------------------------------------------------Exon 1.7a  PDB: A:86-132 (gaps)                ----------------------------------------------------------------------------------------------------------Exon 1.10  PDB: A:239-323 UniProt: 268-352                                           Exon 1.11b  PDB: A:324-354      Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.6c  PDB: A:21-85 UniProt: 50-114                          ----------------------------------------------Exon 1.8  PDB: A:132-174 UniProt: 161-203  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:174-239 UniProt: 203-268                        ------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1ou5 A  -1 DKMKLQSPEFQSLFTEGLKSLTELFVKENHELRIAGGAVRDLLNGVKPQDIDFATTATPTQMKEMFQSAGIRMINNRGEKHGTITARLHEENFEITTLRI------------FTTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVDKPGDHDPETLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSI 354
                                     8        18        28        38        48        58        68        78        88        98         -  |    118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348      
                                                                                                                              98          111                                                                                                                                                                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:344
 aligned with TRNT1_HUMAN | Q96Q11 from UniProtKB/Swiss-Prot  Length:434

    Alignment length:356
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377      
          TRNT1_HUMAN    28 FTMKLQSPEFQSLFTEGLKSLTELFVKENHELRIAGGAVRDLLNGVKPQDIDFATTATPTQMKEMFQSAGIRMINNRGEKHGTITARLHEENFEITTLRIDVTTDGRHAEVEFTTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVDKPGDHDPETLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSI 383
               SCOP domains d1ou5b2 B:-1-150 tRNA CCA-adding enzyme, head domain                                                                                                    d1ou5b1 B:151-354 tRNA CCA-adding enzyme, C-terminal domains                                                                                                                                                 SCOP domains
               CATH domains 1ou5B01 B:-1-150 Beta Polymerase, domain 2                                                                                                              1ou5B02 B:151-354 cca-adding enzyme, domain 2                                                                                                                                                                CATH domains
           Pfam domains (1) -------------------------------PolyA_pol-1ou5B01 B:30-153                                                                                                  --------------------------------PolyA_pol_RNAbd-1ou5B03 B:186-242                        ---------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------PolyA_pol-1ou5B02 B:30-153                                                                                                  --------------------------------PolyA_pol_RNAbd-1ou5B04 B:186-242                        ---------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhh..hhhhhhhhhhhh...eeeehhhhhhhhhh......eeee..hhhhhhhhhh...............eeee......eeee....------------.............hhhhh.ee..........hhhhhh...................hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.....hhhhhhhhhh..hhhhhhhhhhhh.hhhhhh......hhhhhhhhhhhh....hhhhhhhhhh.....hhhhhhhhh...hhhhhhhhhh...............hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------I---V-------S-----------------------I--------------------------------T------------------------------------------------------------------------------------------------------T--------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:-1-21----------------------------------------------------------------Exon 1.7a  PDB: B:86-132 (gaps)                ----------------------------------------------------------------------------------------------------------Exon 1.10  PDB: B:239-323 UniProt: 268-352                                           Exon 1.11b  PDB: B:324-354      Transcript 1 (1)
           Transcript 1 (2) ----------------------Exon 1.6c  PDB: B:21-85 UniProt: 50-114                          ----------------------------------------------Exon 1.8  PDB: B:132-174 UniProt: 161-203  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
           Transcript 1 (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: B:174-239 UniProt: 203-268                        ------------------------------------------------------------------------------------------------------------------- Transcript 1 (3)
                 1ou5 B  -1 DKMKLQSPEFQSLFTEGLKSLTELFVKENHELRIAGGAVRDLLNGVKPQDIDFATTATPTQMKEMFQSAGIRMINNRGEKHGTITARLHEENFEITTLRI------------FTTDWQKDAERRDLTINSMFLGFDGTLFDYFNGYEDLKNKKVRFVGHAKQRIQEDYLRILRYFRFYGRIVDKPGDHDPETLEAIAENAKGLAGISGERIWVELKKILVGNHVNHLIHLIYDLDVAPYIGLPANASLEEFDKVSKNVDGFSPKPVTLLASLFKVQDDVTKLDLRLKIAKEEKNLGLFIVKNRKDLIKATDSSDPLKPYQDFIIDSREPDATTRVCELLKYQGEHCLLKEMQQWSI 354
                                     8        18        28        38        48        58        68        78        88        98         -  |    118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348      
                                                                                                                              98          111                                                                                                                                                                                                                                                   

   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/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TRNT1_HUMAN | Q96Q11)
molecular function
    GO:0034062    5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); the synthesis of RNA from ribonucleotide triphosphates in the presence of a nucleic acid template, via extension of the 3'-end.
    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: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: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:1990180    mitochondrial tRNA 3'-end processing    The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA in the mitochondrion.
    GO:0006626    protein targeting to mitochondrion    The process of directing proteins towards and into the mitochondrion, usually mediated by mitochondrial proteins that recognize signals contained within the imported protein.
    GO:0042780    tRNA 3'-end processing    The process in which the 3' end of a pre-tRNA molecule is converted to that of a mature tRNA.
    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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TRNT1_HUMAN | Q96Q114x4w

(-) Related Entries Specified in the PDB File

1miv CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS CCA-ADDING ENZYME
1miw CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS CCA-ADDING ENZYME
1miy CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS CCA-ADDING ENZYME