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Protein

Pantothenate synthetase

Gene

panC

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate.1 Publication

Catalytic activityi

ATP + (R)-pantoate + beta-alanine = AMP + diphosphate + (R)-pantothenate.1 Publication

Enzyme regulationi

Pantothenate exhibits uncompetitive inhibition toward both D-pantoate and ATP, and non-competitive inhibition toward beta-alanine. AMPCPP exhibits competitive inhibition toward ATP, uncompetitive inhibition toward beta-alanine, and non-competitive inhibition toward D-pantoate. The enzyme is most active in the presence of magnesium or manganese. Other divalent cations (cobalt, nickel, zinc) are less effective.1 Publication

Kineticsi

  1. KM=130 µM for D-pantoate2 Publications
  2. KM=800 µM for beta-alanine2 Publications
  3. KM=2600 µM for ATP2 Publications
  4. KM=25.4 mM for 2-mercaptoethylamine2 Publications
  5. KM=36 mM for carbamate2 Publications
  6. KM=72 mM for 5-aminovalerate2 Publications
  7. KM=79 mM for methylamine2 Publications
  8. KM=84 mM for glycine2 Publications
  9. KM=93 mM for ethylamine2 Publications
  10. KM=103 mM for taurine2 Publications
  11. KM=108 mM for glycolate2 Publications
  12. KM=335 mM for gamma-aminobutyrate2 Publications
  13. KM=580 mM for gamma-amino-beta-hydroxybutyrate2 Publications

    Pathway:i(R)-pantothenate biosynthesis

    This protein is involved in step 1 of the subpathway that synthesizes (R)-pantothenate from (R)-pantoate and beta-alanine.
    Proteins known to be involved in this subpathway in this organism are:
    1. Pantothenate synthetase (panC)
    This subpathway is part of the pathway (R)-pantothenate biosynthesis, which is itself part of Cofactor biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes (R)-pantothenate from (R)-pantoate and beta-alanine, the pathway (R)-pantothenate biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei47 – 471Proton donor
    Binding sitei72 – 721Beta-alanine
    Binding sitei72 – 721Pantoate
    Metal bindingi88 – 881Magnesium
    Metal bindingi89 – 891Magnesium; via amide nitrogen
    Metal bindingi92 – 921Magnesium
    Binding sitei164 – 1641Pantoate
    Binding sitei187 – 1871ATP; via amide nitrogen and carbonyl oxygen1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi40 – 478ATP1 Publication
    Nucleotide bindingi158 – 1614ATP1 Publication
    Nucleotide bindingi195 – 1984ATP1 Publication

    GO - Molecular functioni

    • ATP binding Source: MTBBASE
    • magnesium ion binding Source: MTBBASE
    • manganese ion binding Source: MTBBASE
    • pantoate-beta-alanine ligase activity Source: MTBBASE

    GO - Biological processi

    • beta-alanine metabolic process Source: MTBBASE
    • growth Source: MTBBASE
    • pantothenate biosynthetic process Source: MTBBASE
    Complete GO annotation...

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Pantothenate biosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BRENDAi6.3.2.1. 3445.
    UniPathwayiUPA00028; UER00005.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pantothenate synthetase (EC:6.3.2.1)
    Short name:
    PS
    Alternative name(s):
    Pantoate--beta-alanine ligase
    Pantoate-activating enzyme
    Gene namesi
    Name:panC
    Ordered Locus Names:Rv3602c
    ORF Names:MTCY07H7B.20
    OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
    Taxonomic identifieri83332 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
    ProteomesiUP000001584 Componenti: Chromosome

    Organism-specific databases

    TubercuListiRv3602c.

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi44 – 441H → A: More than 1000-fold reduction in activity and 52-fold decrease in adenylate formation. 1 Publication
    Mutagenesisi47 – 471H → A: More than 1000-fold reduction in activity and 60-fold decrease in adenylate formation. 10-fold decrease in the affinity for ATP. 1 Publication
    Mutagenesisi69 – 691N → A: More than 1000-fold reduction in activity and 50-fold decrease in adenylate formation. 1 Publication
    Mutagenesisi72 – 721Q → A: More than 1000-fold reduction in activity and 45-fold decrease in adenylate formation. 1 Publication
    Mutagenesisi77 – 771E → G: No effect. 1 Publication
    Mutagenesisi160 – 1601K → A: More than 1000-fold reduction in activity and 50-fold decrease in the affinity for ATP. 1 Publication
    Mutagenesisi160 – 1601K → C: More than 1000-fold reduction in activity and 120-fold decrease in adenylate formation. The enzymatic activity and the affinity for beta-alanine can be increased 10- and 3-fold, respectively, by alkylation of cysteine of mutant C-160. 1 Publication
    Mutagenesisi164 – 1641Q → A: 50-fold reduction in activity and slight reduction in the affinity for beta-alanine. 30- and 40-fold decrease in adenylate formation and pantothenate formation, respectively. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed2 Publications
    Chaini2 – 309308Pantothenate synthetasePRO_0000128245Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei2 – 21N-acetylthreonine1 Publication

    Keywords - PTMi

    Acetylation

    Interactioni

    Protein-protein interaction databases

    STRINGi83332.Rv3602c.

    Structurei

    Secondary structure

    1
    309
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi12 – 143Combined sources
    Helixi17 – 2913Combined sources
    Beta strandi33 – 397Combined sources
    Helixi45 – 5511Combined sources
    Beta strandi60 – 667Combined sources
    Helixi70 – 723Combined sources
    Beta strandi75 – 773Combined sources
    Helixi78 – 814Combined sources
    Helixi86 – 9510Combined sources
    Beta strandi100 – 1023Combined sources
    Helixi106 – 1094Combined sources
    Beta strandi116 – 1194Combined sources
    Helixi122 – 1254Combined sources
    Helixi127 – 1293Combined sources
    Helixi135 – 15016Combined sources
    Beta strandi153 – 1586Combined sources
    Helixi159 – 1613Combined sources
    Helixi162 – 17413Combined sources
    Beta strandi180 – 1845Combined sources
    Helixi199 – 2013Combined sources
    Helixi204 – 2096Combined sources
    Helixi212 – 22312Combined sources
    Helixi224 – 2263Combined sources
    Helixi228 – 24013Combined sources
    Beta strandi246 – 2549Combined sources
    Beta strandi258 – 2603Combined sources
    Beta strandi264 – 27411Combined sources
    Beta strandi277 – 28610Combined sources
    Helixi288 – 2903Combined sources
    Beta strandi294 – 2963Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1MOPX-ray1.60A/B3-300[»]
    1N2BX-ray1.70A/B3-300[»]
    1N2EX-ray1.60A/B3-300[»]
    1N2GX-ray1.80A/B3-300[»]
    1N2HX-ray2.00A/B3-300[»]
    1N2IX-ray1.70A/B3-300[»]
    1N2JX-ray1.80A/B3-300[»]
    1N2OX-ray2.10A/B3-300[»]
    2A7XX-ray1.70A3-300[»]
    2A84X-ray1.55A3-300[»]
    2A86X-ray1.85A/B3-300[»]
    2A88X-ray1.70A3-300[»]
    3COVX-ray1.50A/B3-300[»]
    3COWX-ray1.80A/B3-300[»]
    3COYX-ray2.03A/B3-300[»]
    3COZX-ray2.00A/B3-300[»]
    3IMCX-ray1.60A/B3-300[»]
    3IMEX-ray2.39A/B3-300[»]
    3IMGX-ray1.80A/B3-300[»]
    3IOBX-ray1.80A/B3-300[»]
    3IOCX-ray2.50A/B3-300[»]
    3IODX-ray1.75A/B3-300[»]
    3IOEX-ray1.95A/B3-300[»]
    3ISJX-ray2.20A/B3-300[»]
    3IUBX-ray1.50A/B3-301[»]
    3IUEX-ray1.73A/B3-301[»]
    3IVCX-ray2.13A/B3-301[»]
    3IVGX-ray1.95A/B3-301[»]
    3IVXX-ray1.73A/B3-301[»]
    3LE8X-ray1.70A/B3-300[»]
    4DDHX-ray2.07A/B3-301[»]
    4DDKX-ray1.75A/B3-301[»]
    4DDMX-ray1.83A/B3-301[»]
    4DE5X-ray2.25A/B3-301[»]
    4EF6X-ray1.94A/B3-300[»]
    4EFKX-ray1.70A/B3-300[»]
    4FZJX-ray1.63A/B3-301[»]
    4G5FX-ray2.33A/B3-309[»]
    4G5YX-ray1.80A/B3-300[»]
    ProteinModelPortaliP9WIL5.
    SMRiP9WIL5. Positions 3-290.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the pantothenate synthetase family.Curated

    Phylogenomic databases

    KOiK01918.
    OMAiRTTIHPG.
    PhylomeDBiP9WIL5.

    Family and domain databases

    Gene3Di3.40.50.620. 1 hit.
    HAMAPiMF_00158. PanC.
    InterProiIPR003721. Pantoate_ligase.
    IPR014729. Rossmann-like_a/b/a_fold.
    [Graphical view]
    PfamiPF02569. Pantoate_ligase. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00018. panC. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P9WIL5-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTIPAFHPGE LNVYSAPGDV ADVSRALRLT GRRVMLVPTM GALHEGHLAL
    60 70 80 90 100
    VRAAKRVPGS VVVVSIFVNP MQFGAGEDLD AYPRTPDDDL AQLRAEGVEI
    110 120 130 140 150
    AFTPTTAAMY PDGLRTTVQP GPLAAELEGG PRPTHFAGVL TVVLKLLQIV
    160 170 180 190 200
    RPDRVFFGEK DYQQLVLIRQ LVADFNLDVA VVGVPTVREA DGLAMSSRNR
    210 220 230 240 250
    YLDPAQRAAA VALSAALTAA AHAATAGAQA ALDAARAVLD AAPGVAVDYL
    260 270 280 290 300
    ELRDIGLGPM PLNGSGRLLV AARLGTTRLL DNIAIEIGTF AGTDRPDGYR

    AILESHWRN
    Length:309
    Mass (Da):32,678
    Last modified:April 16, 2014 - v1
    Checksum:iEB51DBE3485F970A
    GO

    Mass spectrometryi

    Molecular mass is 32545 Da from positions 2 - 309. Determined by ESI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL123456 Genomic DNA. Translation: CCP46425.1.
    PIRiC70955.
    RefSeqiNP_218119.1. NC_000962.3.
    WP_003419526.1. NZ_KK339374.1.

    Genome annotation databases

    EnsemblBacteriaiCCP46425; CCP46425; Rv3602c.
    GeneIDi885459.
    KEGGimtu:Rv3602c.
    mtv:RVBD_3602c.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL123456 Genomic DNA. Translation: CCP46425.1.
    PIRiC70955.
    RefSeqiNP_218119.1. NC_000962.3.
    WP_003419526.1. NZ_KK339374.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1MOPX-ray1.60A/B3-300[»]
    1N2BX-ray1.70A/B3-300[»]
    1N2EX-ray1.60A/B3-300[»]
    1N2GX-ray1.80A/B3-300[»]
    1N2HX-ray2.00A/B3-300[»]
    1N2IX-ray1.70A/B3-300[»]
    1N2JX-ray1.80A/B3-300[»]
    1N2OX-ray2.10A/B3-300[»]
    2A7XX-ray1.70A3-300[»]
    2A84X-ray1.55A3-300[»]
    2A86X-ray1.85A/B3-300[»]
    2A88X-ray1.70A3-300[»]
    3COVX-ray1.50A/B3-300[»]
    3COWX-ray1.80A/B3-300[»]
    3COYX-ray2.03A/B3-300[»]
    3COZX-ray2.00A/B3-300[»]
    3IMCX-ray1.60A/B3-300[»]
    3IMEX-ray2.39A/B3-300[»]
    3IMGX-ray1.80A/B3-300[»]
    3IOBX-ray1.80A/B3-300[»]
    3IOCX-ray2.50A/B3-300[»]
    3IODX-ray1.75A/B3-300[»]
    3IOEX-ray1.95A/B3-300[»]
    3ISJX-ray2.20A/B3-300[»]
    3IUBX-ray1.50A/B3-301[»]
    3IUEX-ray1.73A/B3-301[»]
    3IVCX-ray2.13A/B3-301[»]
    3IVGX-ray1.95A/B3-301[»]
    3IVXX-ray1.73A/B3-301[»]
    3LE8X-ray1.70A/B3-300[»]
    4DDHX-ray2.07A/B3-301[»]
    4DDKX-ray1.75A/B3-301[»]
    4DDMX-ray1.83A/B3-301[»]
    4DE5X-ray2.25A/B3-301[»]
    4EF6X-ray1.94A/B3-300[»]
    4EFKX-ray1.70A/B3-300[»]
    4FZJX-ray1.63A/B3-301[»]
    4G5FX-ray2.33A/B3-309[»]
    4G5YX-ray1.80A/B3-300[»]
    ProteinModelPortaliP9WIL5.
    SMRiP9WIL5. Positions 3-290.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi83332.Rv3602c.

    Chemistry

    BindingDBiP9WIL5.
    ChEMBLiCHEMBL6069.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCCP46425; CCP46425; Rv3602c.
    GeneIDi885459.
    KEGGimtu:Rv3602c.
    mtv:RVBD_3602c.

    Organism-specific databases

    TubercuListiRv3602c.

    Phylogenomic databases

    KOiK01918.
    OMAiRTTIHPG.
    PhylomeDBiP9WIL5.

    Enzyme and pathway databases

    UniPathwayiUPA00028; UER00005.
    BRENDAi6.3.2.1. 3445.

    Miscellaneous databases

    PROiP9WIL5.

    Family and domain databases

    Gene3Di3.40.50.620. 1 hit.
    HAMAPiMF_00158. PanC.
    InterProiIPR003721. Pantoate_ligase.
    IPR014729. Rossmann-like_a/b/a_fold.
    [Graphical view]
    PfamiPF02569. Pantoate_ligase. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00018. panC. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 25618 / H37Rv.
    2. "Steady-state and pre-steady-state kinetic analysis of Mycobacterium tuberculosis pantothenate synthetase."
      Zheng R., Blanchard J.S.
      Biochemistry 40:12904-12912(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 2-11, FUNCTION, MASS SPECTROMETRY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, REACTION MECHANISM, SUBUNIT.
    3. "Active site residues in Mycobacterium tuberculosis pantothenate synthetase required in the formation and stabilization of the adenylate intermediate."
      Zheng R., Dam T.K., Brewer C.F., Blanchard J.S.
      Biochemistry 43:7171-7178(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF HIS-44; HIS-47; ASN-69; GLN-72; LYS-160 AND GLN-164, BIOPHYSICOCHEMICAL PROPERTIES.
    4. "targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis."
      Raman K., Yeturu K., Chandra N.
      BMC Syst. Biol. 2:109-109(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
    5. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT THR-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
      Strain: ATCC 25618 / H37Rv.
    6. "Crystal structures of a pantothenate synthetase from M. tuberculosis and its complexes with substrates and a reaction intermediate."
      Wang S., Eisenberg D.
      Protein Sci. 12:1097-1108(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 1-300 OF MUTANT GLY-77 IN COMPLEX WITH SUBSTRATES; ATP ANALOG AND MAGNESIUM ION, MUTAGENESIS OF GLU-77, CATALYTIC ACTIVITY, CATALYTIC MECHANISM, SUBUNIT.
    7. "Crystal structure of the pantothenate synthetase from Mycobacterium tuberculosis, snapshots of the enzyme in action."
      Wang S., Eisenberg D.
      Biochemistry 45:1554-1561(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) IN COMPLEX WITH SUBSTRATE; MAGNESIUM ION AND ATP, CATALYTIC MECHANISM, SUBUNIT.

    Entry informationi

    Entry nameiPANC_MYCTU
    AccessioniPrimary (citable) accession number: P9WIL5
    Secondary accession number(s): L0TG74, O06280, P0A5R0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 16, 2014
    Last sequence update: April 16, 2014
    Last modified: July 22, 2015
    This is version 15 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The reaction proceeds by a bi uni uni bi ping pong mechanism.
    Was identified as a high-confidence drug target.

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
      Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.