2A88 - JenaLib

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Title :   CRYSTAL STRUCTURE OF A PANTOTHENATE SYNTHETASE, APO ENZYME IN C2 SPACE GROUP

Authors :   S. Wang, D. Eisenberg, Tb Structural Genomics Consortium (Tbsgc)

Date :   07 Jul 05 (Deposition) - 21 Feb 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Dimer, Rossmann Fold, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Wang, D. Eisenberg
Crystal Structure Of The Pantothenate Synthetase From Mycobacterium Tuberculosis, Snapshots Of The Enzyme In Action.
Biochemistry V. 45 1554 2006
PubMed-ID: 16460002 | Reference-DOI: 10.1021/BI051873E
(for further references see the PDB file header)

Molecule 1 - PANTOATE--BETA-ALANINE LIGASE
	Chains	:	A
	EC Number	:	6.3.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET30A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PANC
	Mutation	:	YES
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	1773
	Synonym	:	PANTOTHENATE SYNTHETASE, PANTOATE ACTIVATING ENZYME

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:44 , LYS A:160 , SER A:196 , SER A:197 , HOH A:2231	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	LEU A:147 , GLN A:148 , ARG A:151 , PRO A:152 , LEU A:177 , ASP A:178	BINDING SITE FOR RESIDUE GOL A 2001
3	AC3	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 A:174	BINDING SITE FOR RESIDUE GOL A 2002

(no "SS Bond" information available for 2A88)

(no "Cis Peptide Bond" information available for 2A88)

(no "SAP(SNP)/Variant" information available for 2A88)

(no "PROSITE Motif" information available for 2A88)

(no "Exon" information available for 2A88)

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
	(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:276
 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 d2a88a_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                         SCOP domains
               CATH domains 2a88A01 A:3-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                  2a88A02 A:186-289  [code=3.30.1300.10, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh....eeeeee.........-----------.hhhhhhhhh...eee..hhhhhh..........hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a88 A   3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGA-----------DDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    12        22        32        42        52        62        72  |      -    |   92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       
                                                                                                   75          87

Chain A from PDB  Type:PROTEIN  Length:276
 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 d2a88a_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                         SCOP domains
               CATH domains 2a88A01 A:3-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                  2a88A02 A:186-289  [code=3.30.1300.10, no name defined]                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee.hhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhh....eeeeee.........-----------.hhhhhhhhh...eee..hhhhhh..........hhhhhhhhhh...hhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...eeeeeeeee.........eeeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a88 A   3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGA-----------DDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIGT 289
                                    12        22        32        42        52        62        72  |      -    |   92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       
                                                                                                   75          87

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 2A88)

Asymmetric Unit(hide GO term definitions)

Chain A (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 (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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	Cis Peptide Bonds
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Biological Unit
	Complete Structure
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	2a88
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	PANC_MYCTO \| P9WIL4
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	PANC_MYCTU \| P9WIL5
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	6.3.2.1
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1mop	STRUCTURE OF THE APO ENZYME IN P21 SPACE GROUP
1n2b	THE SAME ENZYME COMPLEXED WITH AMPCPP AND PANTOATE
1n2h	THE SAME PROTEIN COMPLEXED WITH A REACTION INTERMEDIATE, PANTOYL ADENYLATE RELATED ID: RV3602C RELATED DB: TARGETDB
2a7x	THE SAME ENZYME COMPLEXED WITH AMP
2a84	THE SAME ENZYME COMPLEXED WITH ATP
2a86	THE SAME ENZYME COMPLEXED WITH AMP AND BETA-ALANINE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

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SCOP Domains (1, 1)

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Gene Ontology (13, 20)

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