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(-) Description

Title :  CRYSTAL STRUCTURE OF ADP BOUND PROPIONATE KINASE (TDCD) FROM SALMONELLA TYPHIMURIUM
 
Authors :  D. K. Simanshu, H. S. Savithri, M. R. Murthy
Date :  09 May 05  (Deposition) - 27 Sep 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Propionate Kinase, Tdcd, Adp, L-Threonine Metabolism, Propionate Metabolism, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. K. Simanshu, H. S. Savithri, M. R. Murthy
Crystal Structures Of Adp And Amppnp-Bound Propionate Kinas (Tdcd) From Salmonella Typhimurium: Comparison With Members Of Acetate And Sugar Kinase/Heat Shock Cognate 70/Actin Superfamily.
J. Mol. Biol. V. 352 876 2005
PubMed-ID: 16139298  |  Reference-DOI: 10.1016/J.JMB.2005.07.069

(-) Compounds

Molecule 1 - PROPIONATE KINASE
    ChainsA
    EC Number2.7.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPRSET-C
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneTDCD
    Organism ScientificSALMONELLA TYPHIMURIUM
    Organism Taxid602

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:203 , GLY A:205 , ASN A:206 , ASP A:278 , LEU A:279 , ARG A:280 , GLU A:283 , GLY A:325 , GLY A:326 , ILE A:327 , ASN A:330 , THR A:379 , HOH A:547 , HOH A:551BINDING SITE FOR RESIDUE ADP A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X3M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X3M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X3M)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACETATE_KINASE_1PS01075 Acetate and butyrate kinases family signature 1.TDCD_SALTY7-18  1A:7-18
2ACETATE_KINASE_2PS01076 Acetate and butyrate kinases family signature 2.TDCD_SALTY199-216  1A:199-216
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ACETATE_KINASE_1PS01075 Acetate and butyrate kinases family signature 1.TDCD_SALTY7-18  2A:7-18
2ACETATE_KINASE_2PS01076 Acetate and butyrate kinases family signature 2.TDCD_SALTY199-216  2A:199-216

(-) Exons   (0, 0)

(no "Exon" information available for 1X3M)

(-) 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    
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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
 aligned with TDCD_SALTY | O06961 from UniProtKB/Swiss-Prot  Length:402

    Alignment length:394
                                    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    
           TDCD_SALTY     4 FPVVLVINCGSSSIKFSVLDVATCDVLMAGIADGMNTENAFLSINGDKPINLAHSNYEDALKAIAFELEKRDLTDSVALIGHRIAHGGELFTQSVIITDEIIDNIRRVSPLAPLHNYANLSGIDAARHLFPAVRQVAVFDTSFHQTLAPEAYLYGLPWEYFSSLGVRRYGFHGTSHRYVSRRAYELLDLDEKDSGLIVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDVDFGAMAWIAKETGQTLSDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERARLAIKTFVHRIARHIAGHAASLHRLDGIIFTGGIGENSVLIRQLVIEHLGVLGLTLDVEMNKQPNSHGERIISANPSQVICAVIPTNEEKMIALDAIHLGNVKA 397
               SCOP domains d1x3ma2 A:4-192 Propionate kinase                                                                                                                                                            d1x3ma1 A:193-397 Propionate kinase                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1x3mA02 A:192-397  [code=3.30.420.40, no name defined]                                                                                                                                                         CATH domains
               Pfam domains --Acetate_kinase-1x3mA01 A:6-387                                                                                                                                                                                                                                                                                                                                                                ---------- Pfam domains
         Sec.struct. author ..eeeeeee...eeeeeeee.....eeeeeeee.......eeee.....ee....hhhhhhhhhhhhhhh..hhh.eeeeeeee..........ee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhh...hhhhhhh........hhhhhhhhhhhhhhhh..hhhh.eeeeeee...eeeeeee..eeeee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee........eeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ACETATE_KINA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACETATE_KINASE_2  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x3m 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    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (TDCD_SALTY | O06961)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016774    phosphotransferase activity, carboxyl group as acceptor    Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to a carboxyl group (acceptor).
    GO:0008980    propionate kinase activity    Catalysis of the reaction: ATP + propanoate = ADP + propanoyl phosphate.
    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:0070689    L-threonine catabolic process to propionate    The chemical reactions and pathways resulting in the breakdown of L-threonine (the L-enantiomer of 2-amino-3-hydroxybutyric acid) to form the compound propionate.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006082    organic acid metabolic process    The chemical reactions and pathways involving organic acids, any acidic compound containing carbon in covalent linkage.
    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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TDCD_SALTY | O069611x3n 2e1y 2e1z 2e20 4fwk 4fwl 4fwm 4fwn 4fwo 4fwp 4fwq 4fwr 4fws 4xh1 4xh4 4xh5

(-) Related Entries Specified in the PDB File

1x3n THE SAME PROTEIN WITH ANP