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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TRNAHIS GUANYLYLTRANSFERASE (THG1)- NATIVE II
 
Authors :  S. J. Hyde, B. E. Eckenroth, S. Doublie
Date :  11 Sep 10  (Deposition) - 17 Nov 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Guanylyltransferase, Polymerase-Like Palm Domain, Catalytic Carboxylates, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. J. Hyde, B. E. Eckenroth, B. A. Smith, W. A. Eberley, N. H. Heintz, J. E. Jackman, S. Doublie
Trnahis Guanylyltransferase (Thg1), A Unique 3'-5' Nucleotidyl Transferase, Shares Unexpected Structural Homology With Canonical 5'-3' Dna Polymerases.
Proc. Natl. Acad. Sci. Usa V. 107 20305 2010
PubMed-ID: 21059936  |  Reference-DOI: 10.1073/PNAS.1010436107

(-) Compounds

Molecule 1 - TRNA(HIS) GUANYLYLTRANSFERASE
    ChainsA, B
    EC Number2.7.7.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPME182-FL
    Expression System StrainROSETTA(DE3) PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 30-298
    GeneICF45, THG1L
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainKATO III
    SynonymTRNA-HISTIDINE GUANYLYLTRANSFERASE, INTERPHASE CYTOPLASMIC FOCI PROTEIN 45

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3OTC)

(-) Sites  (0, 0)

(no "Site" information available for 3OTC)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:44 -Pro A:45
2Leu A:227 -Pro A:228
3Lys B:44 -Pro B:45

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_031871L232PTHG1_HUMANPolymorphism2270812A/BL203P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_031871L232PTHG1_HUMANPolymorphism2270812A/BL203P

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OTC)

(-) 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:264
 aligned with THG1_HUMAN | Q9NWX6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:264
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292    
           THG1_HUMAN    33 SKFEYVRDFEADDTCLAHCWVVVRLDGRNFHRFAEKHNFAKPNDSRALQLMTKCAQTVMEELEDIVIAYGQSDEYSFVFKRKTNWFKRRASKFMTHVASQFASSYVFYWRDYFEDQPLLYPPGFDGRVVVYPSNQTLKDYLSWRQADCHINNLYNTVFWALIQQSGLTPVQAQGRLQGTLAADKNEILFSEFNINYNNELPMYRKGTVLIWQKVDEVMTKEIKLPTEMEGKKMAVTRTRTKPVPLHCDIIGDAFWKEHPEILDE 296
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhh.........eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeeee...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhheeeeeeeeeeeeeee..........eeeeeeeeeeeeee......hhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3otc A   4 SKFEYVRDFEADDTCLAHCWVVVRLDGRNFHRFAEKHNFAKPNDSRALQLMTKCAQTVMEELEDIVIAYGQSDEYSFVFKRKTNWFKRRASKFMTHVASQFASSYVFYWRDYFEDQPLLYPPGFDGRVVVYPSNQTLKDYLSWRQADCHINNLYNTVFWALIQQSGLTPVQAQGRLQGTLAADKNEILFSEFNINYNNELPMYRKGTVLIWQKVDEVMTKEIKLPTEMEGKKMAVTRTRTKPVPLHCDIIGDAFWKEHPEILDE 267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263    

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with THG1_HUMAN | Q9NWX6 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:264
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292    
           THG1_HUMAN    33 SKFEYVRDFEADDTCLAHCWVVVRLDGRNFHRFAEKHNFAKPNDSRALQLMTKCAQTVMEELEDIVIAYGQSDEYSFVFKRKTNWFKRRASKFMTHVASQFASSYVFYWRDYFEDQPLLYPPGFDGRVVVYPSNQTLKDYLSWRQADCHINNLYNTVFWALIQQSGLTPVQAQGRLQGTLAADKNEILFSEFNINYNNELPMYRKGTVLIWQKVDEVMTKEIKLPTEMEGKKMAVTRTRTKPVPLHCDIIGDAFWKEHPEILDE 296
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -Thg1-3otcB03 B:5-135                                                                                                               Thg1C-3otcB01 B:136-266                                                                                                            - Pfam domains (1)
           Pfam domains (2) -Thg1-3otcB04 B:5-135                                                                                                               Thg1C-3otcB02 B:136-266                                                                                                            - Pfam domains (2)
         Sec.struct. author ..hhhhhhhh.........eeeeeeee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhh...hhhhhhhhhhhheeeeeee...eee...----......eee....eeeeee.....hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3otc B   4 SKFEYVRDFEADDTCLAHCWVVVRLDGRNFHRFAEKHNFAKPNDSRALQLMTKCAQTVMEELEDIVIAYGQSDEYSFVFKRKTNWFKRRASKFMTHVASQFASSYVFYWRDYFEDQPLLYPPGFDGRVVVYPSNQTLKDYLSWRQADCHINNLYNTVFWALIQQSGLTPVQAQGRLQGTLAADKNEILFSEFNINYNNELPMYRKGTVLIWQKVDEVMTKEI----EMEGKKMAVTRTRTKPVPLHCDIIGDAFWKEHPEILDE 267
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 |    |233       243       253       263    
                                                                                                                                                                                                                                                       225  230                                     

   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 3OTC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (THG1_HUMAN | Q9NWX6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0008193    tRNA guanylyltransferase activity    Catalysis of the posttranscriptional addition of a guanyl residue to the 5' end of a tRNA molecule; observed for His tRNAs.
    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:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0006400    tRNA modification    The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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.

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 Related Entries

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

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        THG1_HUMAN | Q9NWX63otb 3otd 3ote

(-) Related Entries Specified in the PDB File

3otb 3otc 3otd 3ote