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(-) Description

Title :  CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE KINASE (TDCD) IN COMPLEX WITH GDP
 
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 :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase, Kinase, Acetate And Sugar Kinases/Hsc70/Actin (Askha) Superfamily, Tdcd, Gdp, 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:14 , HIS A:118 , LYS A:265 , HOH A:651BINDING SITE FOR RESIDUE EDO A 501
2AC2SOFTWARESER A:166 , HOH A:667BINDING SITE FOR RESIDUE EDO A 502
3AC3SOFTWAREGLY A:205 , 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 , SER A:331BINDING SITE FOR RESIDUE GDP A 503

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FWP)

(-) 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 d4fwpa1 A:4-192 Propionate kinase                                                                                                                                                            d4fwpa2 A:193-397 Propionate kinase                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee.....eeeeeee.......eeeee...eeeee...hhhhhhhhhhhhhhhh.hhh.eeeeeeee..........ee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhhhh.......eeeeeee...eeeeeee..eeeee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee........eeee...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fwp 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 4FWP)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  4fwp
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  TDCD_SALTY | O06961
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  2.7.2.15
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  TDCD_SALTY | O06961
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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 4fwm 4fwn 4fwo 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
4fwm
4fwn
4fwo
4fwq
4fwr
4fws