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(-) Description

Title :  CRYSTAL STRUCTURE OF THYMIDYLATE KINASE FROM STAPHYLOCOCCUS AUREUS BOUND TO INHIBITOR.
 
Authors :  N. A. Larsen, N. B. Olivier
Date :  28 Aug 12  (Deposition) - 24 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Transferase, Nucleotide Binding, Thymidylate Kinase Activity, Atp Binding, Kinase Activity, Transferase Activity, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Martinez-Botella, J. N. Breen, J. E. Duffy, J. Dumas, B. Geng, I. K. Gowers, O. M. Green, S. Guler, M. F. Hentemann, F. A. Hernandez-Juan, D. Joseph-Mccarthy, S. Kawatkar, N. A. Larsen, O. Lazari, J. T. Loch, J. A. Macritchie, A. R. Mckenzie, J. V. Newman, N. B. Olivier, L. G. Otterson, A. P. Owens, J. Read, D. W. Sheppard, T. A. Keating
Discovery Of Selective And Potent Inhibitors Of Gram-Positive Bacterial Thymidylate Kinase (Tmk).
J. Med. Chem. V. 55 10010 2012
PubMed-ID: 23043329  |  Reference-DOI: 10.1021/JM3011806

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: THYMIDYLATE KINASE
    Gene: SA0440, SAR0483, TMK
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 158879
    Strain: MRSA252
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
10Y52Ligand/Ion4-{[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]METHYL}-2-[3-(TRIFLUOROMETHYL)PHENOXY]BENZOIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10Y51Ligand/Ion4-{[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]METHYL}-2-[3-(TRIFLUOROMETHYL)PHENOXY]BENZOIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10Y51Ligand/Ion4-{[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]METHYL}-2-[3-(TRIFLUOROMETHYL)PHENOXY]BENZOIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
10Y52Ligand/Ion4-{[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]METHYL}-2-[3-(TRIFLUOROMETHYL)PHENOXY]BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , GLY A:44 , ARG A:48 , VAL A:51 , LEU A:52 , LEU A:65 , PHE A:66 , SER A:69 , ARG A:70 , ARG A:92 , SER A:97 , TYR A:100 , GLN A:101 , HOH A:484 , HOH A:486 , HOH A:487 , HIS B:172 , SER B:175BINDING SITE FOR RESIDUE 0Y5 A 301
2AC2SOFTWAREGLU B:37 , GLY B:44 , ARG B:48 , VAL B:51 , LEU B:52 , LEU B:65 , PHE B:66 , SER B:69 , ARG B:70 , ARG B:92 , SER B:97 , TYR B:100 , GLN B:101 , HOH B:474 , HOH B:477 , HOH B:478BINDING SITE FOR RESIDUE 0Y5 B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:37 -Pro A:38
2Gly A:54 -Asn A:55
3Glu B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GSY)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GSY)

(-) 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:191
                                                                                                                                                                                                                               
               SCOP domains d4gsya_ 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
                 4gsy A   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIDQEDLKFHEKVIEGYQEIIHQRFKSVNADQPLENVVEDTYQTIIKYLEK 204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 ||    160       170 ||    183       193       203 
                                                                                                                                                                       143|                172|                            
                                                                                                                                                                        153                 176                            


Chain B from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains d4gsyb_ B: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsy 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
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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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GSY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 20)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_STAAN | P65249: 4gfd 4hdc 4hej
        KTHY_STAAR | Q6GJI9: 4hlc 4hld 4qg7 4qga 4qgf 4qgg 4qgh

(-) Related Entries Specified in the PDB File

4f4i APO STRUCTURE OF THYMIDYLATE KINASE FROM STAPHYLOCOCCUS AUREUS.
4hdc
4hej