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(-) Description

Title :  THYMIDYLATE KINASE (TMK) FROM S. AUREUS IN COMPLEX WITH TK-666
 
Authors :  N. B. Olivier, G. Martinez-Botella, T. Keating
Date :  03 Aug 12  (Deposition) - 24 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Thymidine Monphosphate, Soluble, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Keating, J. V. Newman, N. B. Olivier, L. G. Otterson, B. Andrews, P. A. Boriack-Sjodin, J. N. Breen, P. Doig, J. Dumas, E. Gangl, O. M. Green, S. Y. Guler, M. F. Hentemann, D. Joseph-Mccarthy, S. Kawatkar, A. Kutschke, J. T. Loch, A. R. Mckenzie, S. Pradeepan, S. Prasad, G. Martinez-Botella
In Vivo Validation Of Thymidylate Kinase (Tmk) With A Rationally Designed, Selective Antibacterial Compound.
Acs Chem. Biol. V. 7 1866 2012
PubMed-ID: 22908966  |  Reference-DOI: 10.1021/CB300316N

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLH1520
    Expression System Strain: BL21 DE3 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PET30A
    Gene: SA0440, TMK
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 158879
    Strain: STRAIN MU50
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
10YB2Ligand/Ion2-(3-BROMOPHENOXY)-4-{(1R)-3,3-DIMETHYL-1-[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]BUTYL}BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , ARG A:48 , LEU A:52 , PHE A:66 , SER A:69 , ARG A:70 , ARG A:92 , SER A:97 , TYR A:100 , GLN A:101 , HOH A:406 , HOH A:424 , HOH A:429 , HOH A:448 , HIS B:172 , SER B:175BINDING SITE FOR RESIDUE 0YB A 301
2AC2SOFTWAREGLU B:37 , ARG B:48 , LEU B:52 , PHE B:66 , SER B:69 , ARG B:70 , ARG B:92 , SER B:97 , TYR B:100 , GLN B:101 , HOH B:419 , HOH B:449BINDING SITE FOR RESIDUE 0YB B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GFD)

(-) 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 4GFD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GFD)

(-) Exons   (0, 0)

(no "Exon" information available for 4GFD)

(-) 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:189
                                                                                                                                                                                                                             
               SCOP domains d4gfda_ 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.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gfd A   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIDQEDLKFHEKVIEGYQEIIHQRFKSVNADQPLENVVEDTYQTIIKYLEK 204
                                    11        21        31        41        51  ||    63        73        83        93       103       113       123       133       143|      162       172|      185       195         
                                                                               54|                                                                                   143|                172|                            
                                                                                57                                                                                    153                 176                            


Chain B from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains d4gfdb_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gfd B   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51  ||    62        72        82        92       102       112       122       132       142|      162       172       182       192       202   
                                                                               54|                                                                                   142|                                                    
                                                                                56                                                                                    153
   Legend:   → Mismatch (orange background)
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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 4GFD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GFD)

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_STAAM | P65248: 2ccg 2ccj 2cck 4dwj 4eaq 4f4i 4mqb
        KTHY_STAAN | P65249: 4gsy 4hdc 4hej

(-) Related Entries Specified in the PDB File

4dwj CRYSTAL STRUCTURE OF THYMIDYLATE KINASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH THYMIDINE MONOPHOSPHATE
4eaq CRYSTAL STRUCTURE OF THYMIDYLATE KINASE FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH 3'-AZIDO-3'-DEOXYTHYMIDINE-5'- MONOPHOSPHATE
4f4i APO FORM OF SAME PROTEIN FROM STRUCTURAL GENOMICS GROUP
4hdc