3SK3 - JenaLib

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Title :   CRYSTAL STRUCTURE OF SALMONELLA TYPHIMURIUM ACETATE KINASE (ACKA) WITH CITRATE BOUND AT THE DIMERIC INTERFACE

Authors :   S. Chittori, H. S. Savithri, M. R. N. Murthy

Date :   22 Jun 11 (Deposition) - 29 Aug 12 (Release) - 31 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Actin-Like Atpase Domain, Askha Superfamily Of Phosphotransferase, Acetokinase, Atp Binding, Phosphotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chittori, H. S. Savithri, M. R. N. Murthy
Structural And Mechanistic Investigations On Salmonella Typhimurium Acetate Kinase (Acka): Identification Of A Putative Ligand Binding Pocket At The Dimeric Interface
Bmc Struct. Biol. V. 12 24 2012
PubMed-ID: 23031654 | Reference-DOI: 10.1186/1472-6807-12-24

Molecule 1 - ACETATE KINASE
	Chains	:	A, B
	EC Number	:	2.7.2.1
	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	:	ACKA
	Organism Scientific	:	SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM
	Organism Taxid	:	90371
	Strain	:	12529
	Synonym	:	ACETOKINASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:178 , ASP A:257 , THR A:258 , LEU A:259 , GLY A:260 , TYR A:313 , HOH A:422 , HOH A:452 , HOH A:470 , HOH A:478 , HOH A:538 , HOH A:620 , ARG B:309 , LYS B:312 , HOH B:552 , HOH B:608	BINDING SITE FOR RESIDUE CIT A 501
2	AC2	SOFTWARE	TYR A:188 , GLN A:191 , GLU A:192 , GLN A:393	BINDING SITE FOR RESIDUE EDO A 601
3	AC3	SOFTWARE	GLY A:367 , LYS A:368 , SER A:369	BINDING SITE FOR RESIDUE EDO A 604
4	AC4	SOFTWARE	PHE B:187 , GLU B:192 , LYS B:195 , GLN B:393	BINDING SITE FOR RESIDUE EDO B 602
5	AC5	SOFTWARE	VAL B:148 , PHE B:149 , PHE B:153 , THR B:184 , PHE B:187 , ASP B:394 , HOH B:415 , HOH B:420	BINDING SITE FOR RESIDUE EDO B 603

Asymmetric/Biological Unit

No.	Residues
1	A:36	-	A:286
2	B:36	-	B:286

Asymmetric/Biological Unit

No.	Residues
1	Asp A:49	-	Gly A:50

(no "SAP(SNP)/Variant" information available for 3SK3)

Asymmetric/Biological Unit (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.	ACKA_SALTY	6-17	2	A:6-17 B:6-17
2	ACETATE_KINASE_2	PS01076	Acetate and butyrate kinases family signature 2.	ACKA_SALTY	206-223	2	A:206-223 B:206-223

(no "Exon" information available for 3SK3)

Asymmetric/Biological 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:385
 aligned with ACKA_SALTY | P63411 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:398
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392        
           ACKA_SALTY     3 SKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAGAAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFAPLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYGAHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVMGTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAKRAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHERNLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
               SCOP domains d3sk3a1 A:3-199 automated matches                                                                                                                                                                    d3sk3a2 A:200-400 automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee.....eeeeeeee.......eeeeee..eeeeee.....hhhhhhhhhhhh....hhhhhhheeeeeeee..........ee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh....hhhhhhhh......hhhhhhhhhhhhhhhh..hhhhh.eeeee.....eeeeee..eeeee.........-------...hhhhhhhhhhhhh.hhhhhhhhh------.......hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhh.hhhhhhhhhhhhhhhh...hhhhhhhh.....ee........eee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---ACETATE_KINA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACETATE_KINASE_2  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sk3 A   3 SKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAGAAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFAPLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYGAHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEG-------GDIDPAIIFHLHDTLGMSVDQINKML------LGLTEVTSDCRYVEDNYATKEDAKRAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHERNLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    |    -  |    252       262       | -    |  282       292       302       312       322       332       342       352       362       372       382       392        
                                                                                                                                                                                                                                                                    237     245                      270    277

Chain B from PDB  Type:PROTEIN  Length:387
 aligned with ACKA_SALTY | P63411 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:399
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391         
           ACKA_SALTY     2 SSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAGAAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFAPLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYGAHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVMGTRSGDIDPAIIFHLHDTLGMSVDQINKMLTKESGLLGLTEVTSDCRYVEDNYATKEDAKRAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHERNLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
               SCOP domains d3sk3b1 B:2-199 automated matches                                                                                                                                                                     d3sk3b2 B:200-400 automated matches                                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....eeeeeee.....eeeeeeee.......eeeeee..eeeeee.....hhhhhhhhhhhh....hhhhhhheeeeeeee..........ee.hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh....hhhhhh........hhhhhhhhhhhhhhhh..hhhhh.eeeeee...eeeeeee..eeeeee............ee.hhhhhhhhhhhhhhhh....------------hhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhh.hhhhhhhhhhhhhhhh...hhhhhhhh.....ee........eee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----ACETATE_KINA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACETATE_KINASE_2  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sk3 B   2 SSKLVLVLNCGSSSLKFAIIDAVNGDEYLSGLAECFHLPEARIKWKMDGSKQEAALGAGAAHSEALNFIVNTILAQKPELSAQLTAIGHRIVHGGEKYTSSVVIDESVIQGIKDSASFAPLHNPAHLIGIAEALKSFPQLKDKNVAVFDTAFHQTMPEESYLYALPYSLYKEHGVRRYGAHGTSHFYVTQEAAKMLNKPVEELNIITCHLGNGGSVSAIRNGKCVDTSMGLTPLEGLVMGTRSGDIDPAIIFHLHDTLGMSVD------------LGLTEVTSDCRYVEDNYATKEDAKRAMDVYCHRLAKYIGSYTALMDGRLDAVVFTGGIGENAAMVRELSLGKLGVLGFEVDHERNLAARFGKSGFINKEGTRPAVVIPTNEELVIAQDASRLTA 400
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261  |      -     | 281       291       301       311       321       331       341       351       361       371       381       391         
                                                                                                                                                                                                                                                                                                264          277

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: automated matches (111)

Protein domain: automated matches (111)

Salmonella enterica [TaxId: 90371] (2)

1a	d3sk3a1	A:3-199
1b	d3sk3a2	A:200-400
1c	d3sk3b1	B:2-199
1d	d3sk3b2	B:200-400

(no "CATH Domain" information available for 3SK3)

(no "Pfam Domain" information available for 3SK3)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ACKA_SALTY | P63411)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0008776	acetate kinase activity	Catalysis of the reaction: ATP + acetate = ADP + acetyl phosphate.
	GO:0047900	formate kinase activity	Catalysis of the reaction: ATP + formate = ADP + formyl phosphate + H(+).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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:0006085	acetyl-CoA biosynthetic process	The chemical reactions and pathways resulting in the formation of acetyl-CoA, a derivative of coenzyme A in which the sulfhydryl group is acetylated.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:49 - Gly A:50	[ RasMol ]

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	3sk3
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	ACKA_SALTY \| P63411
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	2.7.2.1
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UniProtKB/Swiss-Prot
	ACKA_SALTY \| P63411	:	3slc

1g99	METHANOSARCINA THERMOPHILA ACETATE KINASE
1saz	THERMOTOGA MARITIMA PUTATIVE BUTYRATE KINASE 2
2e1y	SALMONELLA TYPHIMURIUM PROPIONATE KINASE
2iir	THERMOTOGA MARITIMA ACETATE KINASE
3khy	FRANCISELLA TULARENSIS PUTATIVE ACETATE/PROPIONATE KINASE
3p4i	MYCOBACTERIUM AVIUM ACETATE KINASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (2, 2)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 16)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File