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Title :   CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 2.40 ANG RESOLUTION IN COMPLEX WITH FRAGMENT COMPOUND 1-BENZOFURAN-2-CARBOXYLIC ACID

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

Date :   10 Aug 09 (Deposition) - 13 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.39

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

Keywords :   Mycobacterium Tuberculosis, Pantothenate Biosynthesis, Enzymes, Ligase, Drug Design, Fragment-Based, Atp-Binding, Magnesium, Metal- Binding, Nucleotide-Binding (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	:	C41(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-300
	Gene	:	MT3707, MTCY07H7B.20, PANC, RV3602C
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	PS, PANTOATE-BETA-ALANINE LIGASE, PANTOATE-ACTIVATING ENZYME

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	BZ2	2	Ligand/Ion	1-BENZOFURAN-2-CARBOXYLIC ACID
2	EOH	2	Ligand/Ion	ETHANOL
3	GOL	2	Ligand/Ion	GLYCEROL

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:38 , THR A:39 , MET A:40 , HIS A:47 , VAL A:143 , GLN A:164 , HOH A:518	BINDING SITE FOR RESIDUE BZ2 A 301
2	AC2	SOFTWARE	MET A:109 , TYR A:110 , PRO A:111 , ASP A:112 , GLY A:113 , ARG A:115 , THR A:116 , LYS A:145 , ASP B:174	BINDING SITE FOR RESIDUE GOL A 701
3	AC3	SOFTWARE	PRO A:111 , ASP A:112	BINDING SITE FOR RESIDUE GOL A 702
4	AC4	SOFTWARE	ARG A:115 , THR A:117 , GLN B:119 , PRO B:120	BINDING SITE FOR RESIDUE EOH A 703
5	AC5	SOFTWARE	THR A:218 , HIS B:222 , THR B:225	BINDING SITE FOR RESIDUE EOH A 704
6	AC6	SOFTWARE	PRO B:38 , THR B:39 , MET B:40 , HIS B:47 , VAL B:143 , GLN B:164	BINDING SITE FOR RESIDUE BZ2 B 302

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

Asymmetric/Biological Unit

No.	Residues
1	Ala A:75	-	Gly A:76
2	Gly A:76	-	Gly A:77

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

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

(no "Exon" information available for 3IME)

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
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Chain A from PDB  Type:PROTEIN  Length:282
 aligned with PANC_MYCTO | P9WIL4 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:286
                                    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      
           PANC_MYCTO     4 PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
               SCOP domains d3imea_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                        SCOP domains
               CATH domains 3imeA01 A:4-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                 3imeA02 A:186-289  [code=3.30.1300.10, no name defined]                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.hhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh...eeeeeee..................hhhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeee....----.eeeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ime A   4 PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLG----NGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    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      
                                                                                                                                                                                                                                                                                        258  263

Chain A from PDB  Type:PROTEIN  Length:282
 aligned with PANC_MYCTU | P9WIL5 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:286
                                    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      
           PANC_MYCTU     4 PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
               SCOP domains d3imea_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                        SCOP domains
               CATH domains 3imeA01 A:4-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                 3imeA02 A:186-289  [code=3.30.1300.10, no name defined]                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee.hhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh...eeeeeee..................hhhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeeee....----.eeeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ime A   4 PAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGGDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLG----NGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    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      
                                                                                                                                                                                                                                                                                        258  263

Chain B from PDB  Type:PROTEIN  Length:273
 aligned with PANC_MYCTO | P9WIL4 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:287
                                    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 TIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
               SCOP domains d3imeb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, Pan              C)                                                                                                                                                                                                           SCOP domains
               CATH domains 3imeB01 B:2-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                   3imeB02 B:186-288  [code=3.30.1300.10, no name defined]                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhh..eeeeeee....--------------hhhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ime B   2 AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNP--------------TPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
                                    11        21        31        41        51        61        |-         -   |    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       
                                                                                               70             85

Chain B from PDB  Type:PROTEIN  Length:273
 aligned with PANC_MYCTU | P9WIL5 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:287
                                    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 TIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
               SCOP domains d3imeb_ B: Pantothenate synthetase (Pantoate-beta-alanine ligase, Pan              C)                                                                                                                                                                                                           SCOP domains
               CATH domains 3imeB01 B:2-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                   3imeB02 B:186-288  [code=3.30.1300.10, no name defined]                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee.hhhhhhhhhhhhhhh..eeeeeee....hhhhhhhhhhhhhh..eeeeeee....--------------hhhhhhhhhhhhh..eee..hhhhhh......eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh....eeeeeeee..........eeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ime B   2 AIPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNP--------------TPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
                                    11        21        31        41        51        61        |-         -   |    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       
                                                                                               70             85

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 3IME)

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala A:75 - Gly A:76	[ RasMol ]
		Gly A:76 - Gly A:77	[ RasMol ]

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	3ime
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3cov	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 1.5 ANG RESOLUTION- APO FORM
3imc	CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PANTOTHENATE SYNTHETASE AT 1.60 ANG RESOLUTION IN COMPLEX WITH FRAGMENT COMPOUND 5-METHOXYINDOLE, SULFATE AND GLYCEROL
3img	SAME PROTEIN AT 1.8 ANG RESOLUTION IN A TERNARY COMPLEX WITH FRAGMENT COMPOUNDS 5-METHOXYINDOLE AND 1-BENZOFURAN-2- CARBOXYLIC ACID

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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