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(-) Description

Title :  CRYSTAL STRUCTURE OF A PANTOTHENATE SYNTHETASE COMPLEXED WITH AMP
 
Authors :  S. Wang, D. Eisenberg, Tb Structural Genomics Consortium (Tbsgc)
Date :  06 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 :  Protein-Product Inhibitor Complex, 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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2GOL4Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:154 , HOH A:926BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWAREPRO A:38 , MET A:40 , HIS A:44 , GLY A:46 , HIS A:47 , LEU A:50 , PHE A:157 , GLY A:158 , LYS A:160 , ASP A:161 , PRO A:185 , THR A:186 , VAL A:187 , MET A:195 , GOL A:601 , HOH A:738 , HOH A:748 , HOH A:792 , HOH A:829 , HOH A:928BINDING SITE FOR RESIDUE AMP A 501
3AC3SOFTWAREPRO A:38 , THR A:39 , MET A:40 , GLN A:164 , AMP A:501BINDING SITE FOR RESIDUE GOL A 601
4AC4SOFTWARELEU A:147 , GLN A:148 , ARG A:151 , PRO A:152 , LEU A:177 , ASP A:178BINDING SITE FOR RESIDUE GOL A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A7X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A7X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A7X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A7X)

(-) Exons   (0, 0)

(no "Exon" information available for 2A7X)

(-) Sequences/Alignments

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:277
 aligned with PANC_MYCTO | P9WIL4 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:286
                                    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 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
               SCOP domains d2a7xa_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                        SCOP domains
               CATH domains 2a7xA01 A:3-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                  2a7xA02 A:186-288  [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..........eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a7x A   3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGG---------DDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
                                    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      
                                                                                                     77        87                                                                                                                                                                                                         


Chain A from PDB  Type:PROTEIN  Length:277
 aligned with PANC_MYCTU | P9WIL5 from UniProtKB/Swiss-Prot  Length:309

    Alignment length:286
                                    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 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGEDLDAYPRTPDDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
               SCOP domains d2a7xa_ A: Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)                                                                                                                                                                                                                        SCOP domains
               CATH domains 2a7xA01 A:3-185 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                  2a7xA02 A:186-288  [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..........eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a7x A   3 IPAFHPGELNVYSAPGDVADVSRALRLTGRRVMLVPTMGALHEGHLALVRAAKRVPGSVVVVSIFVNPMQFGAGG---------DDDLAQLRAEGVEIAFTPTTAAMYPDGLRTTVQPGPLAAELEGGPRPTHFAGVLTVVLKLLQIVRPDRVFFGEKDYQQLVLIRQLVADFNLDVAVVGVPTVREADGLAMSSRNRYLDPAQRAAAVALSAALTAAAHAATAGAQAALDAARAVLDAAPGVAVDYLELRDIGLGPMPLNGSGRLLVAARLGTTRLLDNIAIEIG 288
                                    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      
                                                                                                     77        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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A7X)

(-) Gene Ontology  (13, 20)

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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PANC_MYCTO | P9WIL4: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o 2a84 2a86 2a88 3cov 3cow 3coy 3coz 3imc 3ime 3img 3iob 3ioc 3iod 3ioe 3isj 3iub 3iue 3ivc 3ivg 3ivx 3le8 4ddh 4ddk 4ddm 4de5 4ef6 4efk 4fzj 4g5f 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul 4mun
        PANC_MYCTU | P9WIL5: 1mop 1n2b 1n2e 1n2g 1n2h 1n2i 1n2j 1n2o 2a84 2a86 2a88 3cov 3cow 3coy 3coz 3imc 3ime 3img 3iob 3ioc 3iod 3ioe 3isj 3iub 3iue 3ivc 3ivg 3ivx 3le8 4ddh 4ddk 4ddm 4de5 4ef6 4efk 4fzj 4g5f 4g5y 4mq6 4mue 4muf 4mug 4muh 4mui 4muj 4muk 4mul 4mun

(-) Related Entries Specified in the PDB File

1mop STRUCTURE OF THE APO ENZYME IN P21 CRYSTAL SPACE GROUP
1n2b THE SAME PROTEIN COMPLEXED WITH AMPCPP AND PANTOATE
1n2g THE SAME PROTEIN COMPLEXED WITH AMPCPP
1n2h THE SAME PROTEIN COMPLEXED WITH A REACTION INTERMEDIATE, PANTOYL ADENYLATE
1n2j THE SAME PROTEIN COMPLEXED WITH PANTOATE RELATED ID: RV3602C RELATED DB: TARGETDB