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Title :   CRYSTAL STRUCTURE OF PANTOTHENATE SYNTHETASE FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH 5-METHOXY-N-(METHYLSULFONYL)-1H-INDOLE-2-CARBOXAMIDE

Authors :   H. L. Silvestre, A. W. Hung, S. Wen, A. Ciulli, T. L. Blundell, C. Abell

Date :   26 Aug 09 (Deposition) - 27 Oct 09 (Release) - 30 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B
Biol. Unit 1: A (1x),B (1x)

Keywords :   Mycobacterium Tuberculosis, Pantothenate Synthetase, Fragment-Based Drug Design, Atp-Binding, Ligase, Magnesium, Metal-Binding, Nucleotide-Binding, Pantothenate Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. W. Hung, H. L. Silvestre, S. Wen, A. Ciulli, T. L. Blundell, C. Abell
Application Of Fragment Growing And Fragment Linking To The Discovery Of Inhibitors Of Mycobacterium Tuberculosis Pantothenate Synthetase
Angew. Chem. Int. Ed. Engl. V. 48 8452 2009
PubMed-ID: 19780086 | Reference-DOI: 10.1002/ANIE.200903821

Molecule 1 - PANTOTHENATE SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.3.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET30A
	Expression System Strain	:	BL21 (ROSETTA 2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PANTOTHENATE SYNTHETASE
	Gene	:	MT3707, MTCY07H7B.20, PANC, RV3602C
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Strain	:	H37RV
	Synonym	:	PS, PANTOATE--BETA-ALANINE LIGASE, PANTOATE-ACTIVATING ENZYME

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 13)

No.	Name	Count	Type	Full Name
1	A8D	2	Ligand/Ion	5-METHOXY-N-(METHYLSULFONYL)-1H-INDOLE-2-CARBOXAMIDE
2	EOH	5	Ligand/Ion	ETHANOL
3	GOL	5	Ligand/Ion	GLYCEROL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	A8D	1	Ligand/Ion	5-METHOXY-N-(METHYLSULFONYL)-1H-INDOLE-2-CARBOXAMIDE
2	EOH	4	Ligand/Ion	ETHANOL
3	GOL	3	Ligand/Ion	GLYCEROL
4	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:115 , THR A:117 , HOH A:315 , GLN B:119 , PRO B:120	BINDING SITE FOR RESIDUE EOH A 302
02	AC2	SOFTWARE	THR A:218 , HIS B:222 , THR B:225	BINDING SITE FOR RESIDUE EOH A 303
03	AC3	SOFTWARE	ASN A:176 , HOH A:447	BINDING SITE FOR RESIDUE EOH A 304
04	AC4	SOFTWARE	MET A:109 , TYR A:110 , PRO A:111 , ASP A:112 , GLY A:113 , LEU A:114 , ARG A:115 , THR A:116 , LYS A:145 , ASP B:174	BINDING SITE FOR RESIDUE GOL A 305
05	AC5	SOFTWARE	ARG A:169 , ARG B:115	BINDING SITE FOR RESIDUE GOL A 306
06	AC6	SOFTWARE	PHE A:67 , GLN A:72 , VAL A:142 , A8D A:308 , HOH A:500	BINDING SITE FOR RESIDUE GOL A 307
07	AC7	SOFTWARE	PRO A:38 , MET A:40 , HIS A:44 , GLY A:46 , HIS A:47 , TYR A:82 , PRO A:185 , THR A:186 , VAL A:187 , MET A:195 , GOL A:307 , HOH A:404	BINDING SITE FOR RESIDUE A8D A 308
08	AC8	SOFTWARE	SER B:24 , ARG B:25 , ARG B:28 , VAL B:34 , VAL B:150 , ARG B:151	BINDING SITE FOR RESIDUE EOH B 301
09	AC9	SOFTWARE	GLY B:244 , ALA B:246 , ARG B:273 , LEU B:274 , GLY B:275	BINDING SITE FOR RESIDUE SO4 B 302
10	BC1	SOFTWARE	LEU B:50 , PHE B:157 , GLY B:158 , LYS B:160 , ASP B:161 , GLN B:164 , A8D B:305 , HOH B:308	BINDING SITE FOR RESIDUE GOL B 303
11	BC2	SOFTWARE	PHE B:67 , GLN B:72 , HOH B:332	BINDING SITE FOR RESIDUE GOL B 304
12	BC3	SOFTWARE	THR B:39 , MET B:40 , HIS B:44 , GLY B:46 , HIS B:47 , PRO B:185 , THR B:186 , VAL B:187 , MET B:195 , GOL B:303	BINDING SITE FOR RESIDUE A8D B 305

(no "SS Bond" information available for 3ISJ)

Asymmetric Unit

No.	Residues
1	Gly A:74	-	Ala A:75
2	Ala A:75	-	Gly A:76

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

(no "PROSITE Motif" information available for 3ISJ)

(no "Exon" information available for 3ISJ)

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:287
 aligned with PANC_MYCTO | P9WIL4 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:287
                                    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       
           PANC_MYCTO     3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
               SCOP domains d3isja_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                         SCOP domains
               CATH domains 3isjA01 A:3-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                  3isjA02 A:186-289  [code=3.30.1300.10, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee..hhhhh...hhhhhh..hhhhhhhhhhhh...eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isj A   3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    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

Chain A from PDB  Type:PROTEIN  Length:287
 aligned with PANC_MYCTU | P9WIL5 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:287
                                    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       
           PANC_MYCTU     3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
               SCOP domains d3isja_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                         SCOP domains
               CATH domains 3isjA01 A:3-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                  3isjA02 A:186-289  [code=3.30.1300.10, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee..hhhhh...hhhhhh..hhhhhhhhhhhh...eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeeee..eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3isj A   3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    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

Chain B from PDB  Type:PROTEIN  Length:279
 aligned with PANC_MYCTO | P9WIL4 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:288
                                    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        
           PANC_MYCTO     2 TIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
               SCOP domains d3isjb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                          SCOP domains
               CATH domains 3isjB01 B:2-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                   3isjB02 B:186-289  [code=3.30.1300.10, no name defined]                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee.......---------..hhhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....eeeeeeee..........eeeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3isj B   2 AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQF---------PRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    11        21        31        41        51        61        71 |       - |      91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
                                                                                                  73        83

Chain B from PDB  Type:PROTEIN  Length:279
 aligned with PANC_MYCTU | P9WIL5 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:288
                                    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        
           PANC_MYCTU     2 TIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
               SCOP domains d3isjb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                          SCOP domains
               CATH domains 3isjB01 B:2-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                   3isjB02 B:186-289  [code=3.30.1300.10, no name defined]                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhh...eeeeeee.......---------..hhhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.....eeeeeeee..........eeeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3isj B   2 AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQF---------PRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    11        21        31        41        51        61        71 |       - |      91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
                                                                                                  73        83

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 '\|'

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (PANC_MYCTO | P9WIL4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	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:0004592	pantoate-beta-alanine ligase activity	Catalysis of the reaction: ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate.
biological process
	GO:0015940	pantothenate biosynthetic process	The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
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,B (PANC_MYCTU | P9WIL5)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) 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:0004592	pantoate-beta-alanine ligase activity	Catalysis of the reaction: ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate.
	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).
biological process
	GO:0019482	beta-alanine metabolic process	The chemical reactions and pathways involving beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins.
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0015940	pantothenate biosynthetic process	The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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