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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE KINASE (TDCD) IN COMPLEX WITH ATP
 
Authors :  S. Chittori, H. S. Savithri, M. R. N. Murthy
Date :  01 Jul 12  (Deposition) - 19 Jun 13  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Kinase, Acetate And Sugar Kinases/Hsc70/Actin (Askha) Superfamily, Propionate Kinase, Tdcd, Short-Chain Fatty Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chittori, D. K. Simanshu, S. Banerjee, A. M. V. Murthy, S. Mathivanan, H. S. Savithri, M. R. N. Murthy
Mechanistic Features Of Salmonella Typhimurium Propionate Kinase (Tdcd): Insights From Kinetic And Crystallographic Studies.
Biochim. Biophys. Acta V. 1834 2036 2013
PubMed-ID: 23747922  |  Reference-DOI: 10.1016/J.BBAPAP.2013.05.020

(-) Compounds

Molecule 1 - PROPIONATE KINASE
    Chains: A
    EC Number: 2.7.2.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: OXD-2, STM3242, TDCD
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2 / SGSC1412 / ATCC 700720

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2EDO8Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:143 , PHE A:174 , HIS A:175 , GLY A:207 , ARG A:236 , ATP A:405BINDING SITE FOR RESIDUE EDO A 401
2AC2SOFTWARETHR A:252BINDING SITE FOR RESIDUE EDO A 402
3AC3SOFTWAREARG A:130BINDING SITE FOR RESIDUE EDO A 404
4AC4SOFTWAREHIS A:175 , HIS A:203 , ASN A:206 , GLY A:207 , ASP A:278 , LEU A:279 , ARG A:280 , GLU A:283 , GLY A:326 , ILE A:327 , ASN A:330 , EDO A:401BINDING SITE FOR RESIDUE ATP A 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FWM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FWM)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4fwma1 A:4-192 automated matches                                                                                                                                                            d4fwma2 A:193-397 automated matches                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee.....eeeeee.........eee.....eee....hhhhhhhhhhhhhhhh.hhh.eeeeeeee..........ee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhhhh..hhhh.eeeeeee...eeeeeee..eeeee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee........eeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fwm A   4 FPVVLVINCGSSSIKFSVLDVATCDVLMAGIADGMNTENAFLSINGDKPINLAHSNYEDALKAIAFELEKRDLTDSVALIGHRIAHGGELFTQSVIITDEIIDNIRRVSPLAPLHNYANLSGIDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLGVRRYGFHGTSHRYVSRRAYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDVDFGAMAWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERARLAIKTFVHRIARHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLGVLGLTLDVEMNKQPNSHGERIISANPSQVICAVIPTNEEKMIALDAIHLGNVKA 397
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
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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 4FWM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  4fwm
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  TDCD_SALTY | O06961
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  2.7.2.15
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 Related Entries

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

UniProtKB/Swiss-Prot
        TDCD_SALTY | O06961: 1x3m 1x3n 2e1y 2e1z 2e20 4fwk 4fwl 4fwn 4fwo 4fwp 4fwq 4fwr 4fws 4xh1 4xh4 4xh5

(-) Related Entries Specified in the PDB File

1x3m CRYSTAL STRUCTURE OF ADP BOUND PROPIONATE KINASE (TDCD) FROM SALMONELLA TYPHIMURIUM
1x3n CRYSTAL STRUCTURE OF AMPPNP BOUND PROPIONATE KINASE (TDCD) FROM SALMONELLA TYPHIMURIUM
2e1y CRYSTAL STRUCTURE OF PROPIONATE KINASE (TDCD) FROM SALMONELLA TYPHIMURIUM
2e1z CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE KINASE (TDCD) IN COMPLEX WITH DIADENOSINE TETRAPHOSPHATE (AP4A) OBTAINED AFTER CO-CRYSTALLIZATION WITH ATP
2e20 CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE KINASE (TDCD) IN COMPLEX WITH DIADENOSINE TETRAPHOSPHATE (AP4A)
4fwk
4fwl
4fwn
4fwo
4fwp
4fwq
4fwr
4fws