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(-) Description

Title :  TERNARY COMPLEX OF THERMUS THERMOPHILUS HB8 URIDINE-CYTIDINE KINASE WITH SUBSTRATES
 
Authors :  F. Tomoike, N. Nakagawa, R. Masui, S. Kuramitsu
Date :  10 Dec 12  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Nucleoside, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Tomoike, N. Nakagawa, R. Masui, S. Kuramitsu
Ternary Complex Of Thermus Thermophilus Hb8 Uridine-Cytidin Kinase With Substrates
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - URIDINE KINASE
    Chains: A, B
    EC Number: 2.7.1.48
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 11A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UDK, TTHA0578
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
    Synonym: CYTIDINE MONOPHOSPHOKINASE, URIDINE MONOPHOSPHOKINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACP2Ligand/IonPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2CTN2Ligand/Ion4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:40 , TYR A:43 , TYR A:59 , ASP A:60 , TYR A:88 , PHE A:90 , TYR A:93 , ILE A:113 , ARG A:142 , ARG A:152 , GLN A:160 , ACP A:302 , HOH A:404 , HOH A:429 , HOH A:499BINDING SITE FOR RESIDUE CTN A 301
2AC2SOFTWARETHR A:15 , ALA A:16 , SER A:17 , GLY A:18 , LYS A:19 , THR A:20 , THR A:21 , ARG A:145 , CTN A:301 , HOH A:477BINDING SITE FOR RESIDUE ACP A 302
3AC3SOFTWAREASP B:40 , TYR B:43 , TYR B:59 , ASP B:60 , TYR B:88 , PHE B:90 , TYR B:93 , ARG B:142 , ARG B:152 , GLN B:160 , ACP B:302 , HOH B:402 , HOH B:410BINDING SITE FOR RESIDUE CTN B 301
4AC4SOFTWAREGLY B:14 , THR B:15 , ALA B:16 , SER B:17 , GLY B:18 , LYS B:19 , THR B:20 , THR B:21 , ARG B:145 , CTN B:301 , HOH B:410BINDING SITE FOR RESIDUE ACP B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3W34)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3W34)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3W34)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3W34)

(-) Exons   (0, 0)

(no "Exon" information available for 3W34)

(-) 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:208
 aligned with URK_THET8 | Q5SKR5 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:208
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        
            URK_THET8     4 PKPFVIGIAGGTASGKTTLAQALARTLGERVALLPMDHYYKDLGHLPLEERLRVNYDHPDAFDLALYLEHAQALLRGLPVEMPVYDFRAYTRSPRRTPVRPAPVVILEGILVLYPKELRDLMDLKVFVDADADERFIRRLKRDVLERGRSLEGVVAQYLEQVKPMHLHFVEPTKRYADVIVPRGGQNPVALEMLAAKALARLARMGAA 211
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhhhhhhhhh..eeeee.hhh.......hhhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeeeee....eeeeeeeee....eeeee......hhhhhh...eeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w34 A   4 PKPFVIGIAGGTASGKTTLAQALARTLGERVALLPMDHYYKDLGHLPLEERLRVNYDHPDAFDLALYLEHAQALLRGLPVEMPVYDFRAYTRSPRRTPVRPAPVVILEGILVLYPKELRDLMDLKVFVDADADERFIRRLKRDVLERGRSLEGVVAQYLEQVKPMHLHFVEPTKRYADVIVPRGGQNPVALEMLAAKALARLARMGAA 211
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with URK_THET8 | Q5SKR5 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:203
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204   
            URK_THET8     5 KPFVIGIAGGTASGKTTLAQALARTLGERVALLPMDHYYKDLGHLPLEERLRVNYDHPDAFDLALYLEHAQALLRGLPVEMPVYDFRAYTRSPRRTPVRPAPVVILEGILVLYPKELRDLMDLKVFVDADADERFIRRLKRDVLERGRSLEGVVAQYLEQVKPMHLHFVEPTKRYADVIVPRGGQNPVALEMLAAKALARLAR 207
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhh..eeeee.hhh.......hhhhhhhh...hhhhhhhhhhhhhhhhhhh...eee..ee....ee....eee....eeeee......hhhhhh...eeeeee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w34 B   5 KPFVIGIAGGTASGKTTLAQALARTLGERVALLPMDHYYKDLGHLPLEERLRVNYDHPDAFDLALYLEHAQALLRGLPVEMPVYDFRAYTRSPRRTPVRPAPVVILEGILVLYPKELRDLMDLKVFVDADADERFIRRLKRDVLERGRSLEGVVAQYLEQVKPMHLHFVEPTKRYADVIVPRGGQNPVALEMLAAKALARLAR 207
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3W34)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3W34)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3W34)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (URK_THET8 | Q5SKR5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0016773    phosphotransferase activity, alcohol group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
    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.
    GO:0004849    uridine kinase activity    Catalysis of the reaction: ATP + uridine = ADP + UMP.
biological process
    GO:0044211    CTP salvage    Any process which produces cytidine 5'-triphosphate (CTP) from derivatives of it, without de novo synthesis.
    GO:0044206    UMP salvage    Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0008655    pyrimidine-containing compound salvage    Any process that generates a pyrimidine-containing compound, any nucleobase, nucleoside, nucleotide or nucleic acid that contains a pyrimidine base, from derivatives of them without de novo synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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UniProtKB/Swiss-Prot
        URK_THET8 | Q5SKR5: 3asy 3asz 3w8r

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