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Title :   PANTOTHENATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS (MTPANK) IN COMPLEX WITH A COENZYME A DERIVATIVE, FORM-II (LT)

Authors :   S. Das, P. Kumar, V. Bhor, A. Surolia, M. Vijayan

Date :   20 Mar 06 (Deposition) - 06 Jun 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Homodimer, Coa Biosynthesis, Nucleotide Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Das, P. Kumar, V. Bhor, A. Surolia, M. Vijayan
Invariance And Variability In Bacterial Pank: A Study Based On The Crystal Structure Of Mycobacterium Tuberculosis Pank
Acta Crystallogr. , Sect. D V. 62 628 2006
PubMed-ID: 16699190 | Reference-DOI: 10.1107/S0907444906012728
(for further references see the PDB file header)

Molecule 1 - PANTOTHENATE KINASE
	Chains	:	A
	EC Number	:	2.7.1.33
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET-28A(+) (NOVAGEN)
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	COAA(RV1092C)
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	PANK, PANTOTHENIC ACID KINASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CME	1	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	COK	1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-4-{[3-({2-[(2-HYDROXYETHYL)DITHIO]ETHYL}AMINO)-3-OXOPROPYL]AMINO}-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE
3	GOL	6	Ligand/Ion	GLYCEROL
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (4, 18)

No.	Name	Count	Type	Full Name
1	CME	2	Mod. Amino Acid	S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2	COK	2	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-4-{[3-({2-[(2-HYDROXYETHYL)DITHIO]ETHYL}AMINO)-3-OXOPROPYL]AMINO}-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE
3	GOL	12	Ligand/Ion	GLYCEROL
4	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:39 , VAL A:99 , ALA A:100 , LYS A:103 , SER A:104 , ARG A:108 , ASP A:129 , LYS A:147 , TYR A:177 , HIS A:179 , TYR A:182 , LEU A:203 , TYR A:235 , ARG A:238 , PHE A:239 , MET A:242 , ALA A:246 , PHE A:247 , PHE A:254 , ILE A:272 , ILE A:276 , ASN A:277 , HOH A:613 , HOH A:691 , HOH A:715 , HOH A:751 , HOH A:764 , HOH A:765 , HOH A:767 , TRS A:5080	BINDING SITE FOR RESIDUE COK A 401
2	AC2	SOFTWARE	GLY A:36 , LEU A:37 , ARG A:38 , ARG A:108 , ARG A:140 , COK A:401 , HOH A:715	BINDING SITE FOR RESIDUE TRS A 5080
3	AC3	SOFTWARE	THR A:127 , ASP A:129 , GLY A:130 , TYR A:177 , HOH A:716	BINDING SITE FOR RESIDUE GOL A 901
4	AC4	SOFTWARE	ARG A:15 , GLN A:43 , ASP A:45 , GLU A:48 , SER A:303	BINDING SITE FOR RESIDUE GOL A 902
5	AC5	SOFTWARE	SER A:215 , PHE A:218 , SER A:221 , ARG A:291 , THR A:293 , ARG A:310 , HOH A:592	BINDING SITE FOR RESIDUE GOL A 903
6	AC6	SOFTWARE	CME A:173 , GLY A:187 , GLU A:189 , ALA A:248 , HIS A:255 , HOH A:630 , HOH A:653	BINDING SITE FOR RESIDUE GOL A 904
7	AC7	SOFTWARE	ALA A:115 , PRO A:121 , ARG A:122 , VAL A:123 , HOH A:722	BINDING SITE FOR RESIDUE GOL A 905
8	AC8	SOFTWARE	ARG A:160 , PHE A:161 , SER A:164 , ALA A:172 , CME A:173 , PRO A:250	BINDING SITE FOR RESIDUE GOL A 906

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

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

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

(no "PROSITE Motif" information available for 2GEV)

(no "Exon" information available for 2GEV)

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:308
 aligned with COAA_MYCTO | P9WPA6 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:308
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304        
           COAA_MYCTO     5 SEPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYACAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL 312
               SCOP domains d2geva_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2gevA00 A:5-312 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeee....hhhhhhhhhhhhhhh......eeeee.hhhh.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeeeee....eeeee...........hhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gev A   5 SEPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYAcAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL 312
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304        
                                                                                                                                                                                                  173-CME

Chain A from PDB  Type:PROTEIN  Length:308
 aligned with COAA_MYCTU | P9WPA7 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:308
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304        
           COAA_MYCTU     5 SEPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYACAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL 312
               SCOP domains d2geva_ A: automated matches                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2gevA00 A:5-312 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeehhhhhhhhh......hhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeeee....hhhhhhhhhhhhhhh......eeeee.hhhh.hhhhhhhh.......hhhhhhhhhhhhhhhhhhh....eeeeeee....eeeeeeeeee....eeeee...........hhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gev A   5 SEPSPYVEFDRRQWRALRMSTPLALTEEELVGLRGLGEQIDLLEVEEVYLPLARLIHLQVAARQRLFAATAEFLGEPQQNPDRPVPFIIGVAGSVAVGKSTTARVLQALLARWDHHPRVDLVTTDGFLYPNAELQRRNLMHRKGFPESYNRRALMRFVTSVKSGSDYAcAPVYSHLHYDIIPGAEQVVRHPDILILEGLNVLQTGPTLMVSDLFDFSLYVDARIEDIEQWYVSRFLAMRTTAFADPESHFHHYAAFSDSQAVVAAREIWRTINRPNLVENILPTRPRATLVLRKDADHSINRLRLRKL 312
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304        
                                                                                                                                                                                                  173-CME

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( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: automated matches (303)

Protein domain: automated matches (303)

Mycobacterium tuberculosis [TaxId: 83332] (20)

d2geva_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Mycobacterium tuberculosis h37rv. Organism_taxid: 83332. Strain: h37rv. (5)

2gevA00

A:5-312

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

Asymmetric Unit(hide GO term definitions)

Chain A (COAA_MYCTO | P9WPA6)

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: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:0004594	pantothenate kinase activity	Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate.
	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:0015937	coenzyme A biosynthetic process	The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
	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: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.

Chain A (COAA_MYCTU | P9WPA7)

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: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:0004594	pantothenate kinase activity	Catalysis of the reaction: ATP + pantothenate = ADP + D-4'-phosphopantothenate.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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.
	GO:0004849	uridine kinase activity	Catalysis of the reaction: ATP + uridine = ADP + UMP.
biological process
	GO:0015937	coenzyme A biosynthetic process	The chemical reactions and pathways resulting in the formation of coenzyme A, 3'-phosphoadenosine-(5')diphospho(4')pantatheine, an acyl carrier in many acylation and acyl-transfer reactions in which the intermediate is a thiol ester.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	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: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.
	GO:0006206	pyrimidine nucleobase metabolic process	The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
	GO:0043097	pyrimidine nucleoside salvage	Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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2ges	THE SAME PROTEIN COMPLEXED WITH A COENZYME A DERIVATIVE, FORM-I (RT)
2get	THE SAME PROTEIN COMPLEXED WITH A COENZYME A DERIVATIVE, FORM-I (LT)
2geu	THE SAME PROTEIN COMPLEXED WITH A COENZYME A DERIVATIVE, FORM-II (RT)

Description

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Ligands, Modified Residues, Ions (4, 9)

Sites (8, 8)

SS Bonds (0, 0)

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