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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDYLATE KINASE (AQ_969) FROM AQUIFEX AEOLICUS VF5
 
Authors :  J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, N. Nakaga A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken St Genomics/Proteomics Initiative (Rsgi)
Date :  29 Mar 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Kinase, Transferase, Nucleotide Biosynthesis, Tmp-Binding, Atp- Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, N. Nakagawa, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of Thymidylate Kinase (Aq_969) From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    ChainsA, B
    EC Number2.7.4.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A
    Expression System StrainBL-21 CONDON PLUS (DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificAQUIFEX AEOLICUS
    Organism Taxid224324
    StrainVF5
    SynonymDTMP KINASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 2PBR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PBR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:36 -Pro A:37
2Glu B:36 -Pro B:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PBR)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_AQUAE87-99
 
  2A:87-99
B:87-99
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_AQUAE87-99
 
  2A:87-99
B:87-99
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_AQUAE87-99
 
  2A:87-99
B:87-99

(-) Exons   (0, 0)

(no "Exon" information available for 2PBR)

(-) 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:195
 aligned with KTHY_AQUAE | O67099 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
           KTHY_AQUAE     1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
               SCOP domains d2pbra_ A: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------THYMIDYLATE_K------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbr A   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with KTHY_AQUAE | O67099 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     
           KTHY_AQUAE     1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
               SCOP domains d2pbrb_ B: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Thymidylate_kin-2pbrB01 B:5-185                                                                                                                                                      ---------- Pfam domains (1)
           Pfam domains (2) ----Thymidylate_kin-2pbrB02 B:5-185                                                                                                                                                      ---------- Pfam domains (2)
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhh.....hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------THYMIDYLATE_K------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pbr B   1 MLIAFEGIDGSGKTTQAKKLYEYLKQKGYFVSLYREPGGTKVGEVLREILLTEELDERTELLLFEASRSKLIEEKIIPDLKRDKVVILDRFVLSTIAYQGYGKGLDVEFIKNLNEFATRGVKPDITLLLDIPVDIALRRLKEKNRFENKEFLEKVRKGFLELAKEEENVVVIDASGEEEEVFKEILRALSGVLRV 195
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190     

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PBR)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KTHY_AQUAE | O67099)
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:0004798    thymidylate kinase activity    Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
    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:0009041    uridylate kinase activity    Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
    GO:0006233    dTDP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
    GO:0006235    dTTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
    GO:0006227    dUDP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    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.
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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        KTHY_AQUAE | O670994s2e 4s35 5h56 5h5b 5h5k 5xai 5xb2 5xb3 5xb5 5xbh

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