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Title :   CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM PROPIONATE KINASE (TDCD) IN COMPLEX WITH DIADENOSINE TETRAPHOSPHATE (AP4A)

Authors :   D. K. Simanshu, H. S. Savithri, M. R. N. Murthy

Date :   04 Nov 06 (Deposition) - 18 Sep 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Propionate Kinase, Tdcd, Native, Acetate Kinase, Nucleotide, Ap4A, Adp, Atp, Amppnp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. K. Simanshu, H. S. Savithri, M. R. N. Murthy
Crystal Structures Of Salmonella Typhimurium Propionate Kinase And Its Complex With Ap4A: Evidence For A Novel Ap4A Synthetic Activity.
Proteins V. 70 1379 2008
PubMed-ID: 17894350 | Reference-DOI: 10.1002/PROT.21626
(for further references see the PDB file header)

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)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TDCD
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602
	Strain	:	IFO 12529

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	B4P	1	Ligand/Ion	BIS(ADENOSINE)-5'-TETRAPHOSPHATE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	B4P	2	Ligand/Ion	BIS(ADENOSINE)-5'-TETRAPHOSPHATE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:11 , ARG A:86 , ALA A:88 , HIS A:118 , HIS A:175 , HIS A:203 , GLY A:205 , ASN A:206 , GLY A:207 , PRO A:227 , ASP A:278 , LEU A:279 , ARG A:280 , GLU A:283 , GLY A:326 , ILE A:327 , ASN A:330 , EDO A:404 , HOH A:463 , HOH A:524 , HOH A:530 , HOH A:532 , HOH A:533 , HOH A:548	BINDING SITE FOR RESIDUE B4P A 403
2	AC2	SOFTWARE	PHE A:174 , HIS A:175 , GLY A:207 , MET A:223 , PRO A:227 , ARG A:236 , B4P A:403 , HOH A:523	BINDING SITE FOR RESIDUE EDO A 404

(no "SS Bond" information available for 2E20)

(no "Cis Peptide Bond" information available for 2E20)

(no "SAP(SNP)/Variant" information available for 2E20)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACETATE_KINASE_1	PS01075	Acetate and butyrate kinases family signature 1.	TDCD_SALTY	7-18	1	A:7-18
2	ACETATE_KINASE_2	PS01076	Acetate and butyrate kinases family signature 2.	TDCD_SALTY	199-216	1	A:199-216

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACETATE_KINASE_1	PS01075	Acetate and butyrate kinases family signature 1.	TDCD_SALTY	7-18	2	A:7-18
2	ACETATE_KINASE_2	PS01076	Acetate and butyrate kinases family signature 2.	TDCD_SALTY	199-216	2	A:199-216

(no "Exon" information available for 2E20)

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
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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 d2e20a1 A:4-192 Propionate kinase                                                                                                                                                            d2e20a2 A:193-397 Propionate kinase                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2e20A02 A:192-397  [code=3.30.420.40, no name defined]                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee........eeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ACETATE_KINA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACETATE_KINASE_2  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e20 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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: Acetokinase-like (17)

Protein domain: Propionate kinase (12)

Salmonella typhimurium [TaxId: 90371] (12)

1a	d2e20a1	A:4-192
1b	d2e20a2	A:193-397

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.40, no name defined] (217)

Salmonella typhimurium. Organism_taxid: 602. Strain: ifo 12529. (3)

2e20A02

A:192-397

(no "Pfam Domain" information available for 2E20)

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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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

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