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(-) Description

Title :  CRYSTAL STRUCTURE OF S. AUREUS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE
 
Authors :  M. Kotaka, B. Dhaliwal, J. Ren, C. E. Nichols, R. Angell, M. Lockyer, A. R. Hawkins, D. K. Stammers
Date :  16 Jan 06  (Deposition) - 08 Mar 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Transferase, Nucleotide Biosynthesis, Tmp-Binding, Atp-Binding, Thymidylate Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Kotaka, B. Dhaliwal, J. Ren, C. E. Nichols, R. Angell, M. Lockyer, A. R. Hawkins, D. K. Stammers
Structures Of S. Aureus Thymidylate Kinase Reveal An Atypical Active Site Configuration And An Intermediate Conformational State Upon Substrate Binding
Protein Sci. V. 15 774 2006
PubMed-ID: 16522804  |  Reference-DOI: 10.1110/PS.052002406

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3TMP3Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:132 , ASN A:182 , HOH B:2080BINDING SITE FOR RESIDUE CL A1206
02AC2SOFTWAREARG A:36 , GLY A:39 , LYS A:77 , HOH A:2015BINDING SITE FOR RESIDUE CL A1207
03AC3SOFTWARELEU A:187 , HOH B:2142BINDING SITE FOR RESIDUE CL A1208
04AC4SOFTWAREHOH A:2149 , LEU B:187BINDING SITE FOR RESIDUE CL B1206
05AC5SOFTWAREGLU A:53 , ASN B:132 , VAL B:181 , ASN B:182 , HOH B:2170BINDING SITE FOR RESIDUE CL B1207
06AC6SOFTWARELYS A:15 , GLU A:37 , PHE A:66 , ARG A:70 , ARG A:92 , SER A:97 , TYR A:100 , GLN A:101 , HOH A:2102 , HOH A:2105 , HOH A:2109 , HOH A:2216BINDING SITE FOR RESIDUE TMP A1209
07AC7SOFTWAREARG A:71 , LEU A:74 , ILE A:120 , ASN A:121BINDING SITE FOR RESIDUE EDO A1210
08AC8SOFTWAREGLU B:11 , LYS B:15 , ARG B:36 , ARG B:70 , ARG B:92 , SER B:96 , SER B:97 , TYR B:100 , GLN B:101 , TMP B:1209 , HOH B:2011 , HOH B:2115 , HOH B:2194 , HOH B:2195BINDING SITE FOR RESIDUE TMP B1208
09AC9SOFTWAREALA B:63 , PHE B:66 , GLN B:101 , ARG B:105 , TMP B:1208 , HOH B:2066 , HOH B:2092 , HOH B:2115 , HOH B:2195 , HOH B:2197BINDING SITE FOR RESIDUE TMP B1209
10BC1SOFTWAREARG B:71 , ILE B:120 , ASN B:121BINDING SITE FOR RESIDUE EDO B1210
11BC2SOFTWAREGLU B:37 , ARG B:48 , PHE B:66 , SER B:69 , ARG B:70BINDING SITE FOR RESIDUE EDO B1211

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:37 -Pro A:38
2Glu B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_KINASEPS01331 Thymidylate kinase signature.KTHY_STAAM89-101
 		  2A:89-101
B:89-101

(-) Exons   (0, 0)

(no "Exon" information available for 2CCJ)

(-) 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:197
 aligned with KTHY_STAAM | P65248 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
           KTHY_STAAM     2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSRDQNRLDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
               SCOP domains d2ccja_ A: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh.---...hhhhhhhhhhhhhhhhhhhh----.eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------THYMIDYLATE_K-------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ccj A   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNS---NRLDQEDLKFHEKVIEGYQEIIH----RFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    |  151       161       171|    | 181       191       201    
                                                                                                                                                                          146 150                   172  177                            


Chain B from PDB  Type:PROTEIN  Length:196
 aligned with KTHY_STAAM | P65248 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201    
           KTHY_STAAM     2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSRDQNRLDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
               SCOP domains d2ccjb_ B: automated matches                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh----...hhhhhhhhhhhhhhhhhhh----..eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------THYMIDYLATE_K-------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ccj B   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKN----NRLDQEDLKFHEKVIEGYQEII----QRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   |   151       161       171    |  181       191       201    
                                                                                                                                                                         145  150                  171  176
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CCJ)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (KTHY_STAAM | P65248)
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.
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_STAAM | P65248: 2ccg 2cck 4dwj 4eaq 4f4i 4gfd 4mqb

(-) Related Entries Specified in the PDB File

2ccg CRYSTAL STRUCTURE OF HIS-TAGGED S. AUREUS THYMIDYLATE KINASE COMPLEXED WITH THYMIDINE MONOPHOSPHATE (TMP)
2cck CRYSTAL STRUCTURE OF UNLIGANDED S. AUREUS THYMIDYLATE KINASE