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Protein

D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase

Gene

gmhB

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate (beta-HBP) intermediate into D-glycero-beta-D-manno-heptose 1-phosphate by removing the phosphate group at the C-7 position.3 Publications

Catalytic activityi

D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O = D-glycero-beta-D-manno-heptose 1-phosphate + phosphate.4 Publications

Cofactori

Protein has several cofactor binding sites:

Kineticsi

kcat is 35.7 sec(-1) and 4.6 sec(-1) with beta-HBP and alpha-HBP as substrate, respectively. Thus, the enzyme displays 100-fold more efficiency towards the beta- than the alpha-anomer (PubMed:20050615). kcat is 0.51 sec(-1) and 0.039 sec(-1) with sedoheptulose-1,7-bisphosphate and fructose-1,6-bisphosphate as substrate, respectively (PubMed:20050615).1 Publication

  1. KM=5 µM for beta-HBP (at pH 7.5 and 25 degrees Celsius)3 Publications
  2. KM=67 µM for alpha-HBP (at pH 7.5 and 25 degrees Celsius)3 Publications
  3. KM=0.20 mM for HBP (at pH 8)3 Publications
  4. KM=0.42 mM for fructose-1,6-bisphosphate (at pH 9)3 Publications
  5. KM=610 µM for sedoheptulose-1,7-bisphosphate (at pH 7.5)3 Publications
  6. KM=1501 µM for fructose-1,6-bisphosphate (at pH 7.5)3 Publications

    pH dependencei

    Optimum pH is between 6 and 7.5.2 Publications

    Pathwayi: ADP-L-glycero-beta-D-manno-heptose biosynthesis

    This protein is involved in step 2 of the subpathway that synthesizes ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate.3 Publications
    Proteins known to be involved in the 4 steps of the subpathway in this organism are:
    1. Bifunctional protein HldE (hldE)
    2. D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase (gmhB)
    3. Bifunctional protein HldE (hldE)
    4. ADP-L-glycero-D-manno-heptose-6-epimerase (hldD)
    This subpathway is part of the pathway ADP-L-glycero-beta-D-manno-heptose biosynthesis, which is itself part of Nucleotide-sugar biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes ADP-L-glycero-beta-D-manno-heptose from D-glycero-beta-D-manno-heptose 7-phosphate, the pathway ADP-L-glycero-beta-D-manno-heptose biosynthesis and in Nucleotide-sugar biosynthesis.

    Pathwayi: LPS core biosynthesis

    This protein is involved in the pathway LPS core biosynthesis, which is part of Bacterial outer membrane biogenesis.2 Publications
    View all proteins of this organism that are known to be involved in the pathway LPS core biosynthesis and in Bacterial outer membrane biogenesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei11 – 111Nucleophile1 Publication
    Metal bindingi11 – 111Magnesium1 Publication
    Active sitei13 – 131Proton donor2 Publications
    Metal bindingi13 – 131Magnesium; via carbonyl oxygen1 Publication
    Sitei53 – 531Stabilizes the phosphoryl group2 Publications
    Metal bindingi92 – 921Zinc1 Publication
    Metal bindingi94 – 941Zinc; via amide nitrogen1 Publication
    Metal bindingi107 – 1071Zinc1 Publication
    Metal bindingi109 – 1091Zinc1 Publication
    Sitei110 – 1101Contributes to substrate recognition1 Publication
    Sitei111 – 1111Stabilizes the phosphoryl group1 Publication
    Metal bindingi136 – 1361Magnesium1 Publication
    Metal bindingi137 – 1371Magnesium1 Publication
    Binding sitei137 – 1371Substrate1 Publication

    GO - Molecular functioni

    • D,D-heptose 1,7-bisphosphate phosphatase activity Source: UniProtKB
    • magnesium ion binding Source: UniProtKB
    • zinc ion binding Source: UniProtKB

    GO - Biological processi

    • ADP-L-glycero-beta-D-manno-heptose biosynthetic process Source: UniProtKB-UniPathway
    • lipopolysaccharide core region biosynthetic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism, Lipopolysaccharide biosynthesis

    Keywords - Ligandi

    Magnesium, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11736-MONOMER.
    ECOL316407:JW0196-MONOMER.
    MetaCyc:EG11736-MONOMER.
    BRENDAi3.1.3.82. 2026.
    UniPathwayiUPA00356; UER00438.
    UPA00958.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase (EC:3.1.3.824 Publications)
    Alternative name(s):
    D,D-heptose 1,7-bisphosphate phosphatase
    Short name:
    HBP phosphatase
    Gene namesi
    Name:gmhB
    Synonyms:yaeD
    Ordered Locus Names:b0200, JW0196
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11736. gmhB.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Cells lacking this gene result in the formation of an altered LPS core, but does not appear to disrupt full-length LPS production to an extent that the outer membrane permeability barrier is compromised.2 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi11 – 111D → N: Inactive. 1 Publication
    Mutagenesisi13 – 131D → A: Inactive. 2 Publications
    Mutagenesisi13 – 131D → N: Inactive. 2 Publications
    Mutagenesisi92 – 921C → A: Reduces the catalytic efficiencies towards the alpha and beta-anomers of HBP. 1 Publication
    Mutagenesisi107 – 1071C → A: More than 3-fold reduction in the affinity binding of HBP. Reduces the catalytic efficiencies towards the alpha and beta-anomers of HBP. 2 Publications
    Mutagenesisi109 – 1091C → A: Reduces the catalytic efficiencies towards the alpha and beta-anomers of HBP. 1 Publication
    Mutagenesisi110 – 1101R → A: Significant reduction in the catalytic efficiency of hydrolysis of the physiological substrate HBP. 1 Publication
    Mutagenesisi111 – 1111K → N: Inactive. 1 Publication
    Mutagenesisi137 – 1371K → A: 8-fold reduction in the affinity binding of HBP. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 191191D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatasePRO_0000209389Add
    BLAST

    Proteomic databases

    PaxDbiP63228.
    PRIDEiP63228.

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Protein-protein interaction databases

    BioGridi4259752. 280 interactions.
    DIPiDIP-47998N.
    IntActiP63228. 11 interactions.
    STRINGi511145.b0200.

    Structurei

    Secondary structure

    1
    191
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 104Combined sources
    Turni13 – 153Combined sources
    Helixi26 – 283Combined sources
    Helixi35 – 4410Combined sources
    Beta strandi48 – 547Combined sources
    Helixi57 – 604Combined sources
    Helixi65 – 8117Combined sources
    Beta strandi87 – 926Combined sources
    Helixi101 – 1033Combined sources
    Beta strandi108 – 1103Combined sources
    Helixi115 – 12410Combined sources
    Helixi128 – 1303Combined sources
    Beta strandi132 – 1376Combined sources
    Helixi138 – 1469Combined sources
    Beta strandi150 – 15910Combined sources
    Helixi163 – 1686Combined sources
    Beta strandi170 – 1745Combined sources
    Helixi176 – 1783Combined sources
    Helixi179 – 1846Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GMWX-ray1.50A/B1-191[»]
    3ESQX-ray1.70A1-191[»]
    3ESRX-ray1.95A1-191[»]
    3L1UX-ray1.95A/B1-191[»]
    3L1VX-ray1.95A/B1-191[»]
    3L8EX-ray1.64A/B1-187[»]
    3L8FX-ray1.79A1-187[»]
    3L8GX-ray2.18A1-187[»]
    ProteinModelPortaliP63228.
    SMRiP63228. Positions 4-187.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP63228.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni11 – 133Substrate binding2 Publications
    Regioni19 – 224Substrate binding1 Publication
    Regioni53 – 564Substrate binding2 Publications
    Regioni110 – 1112Substrate binding1 Publication

    Sequence similaritiesi

    Belongs to the GmhB family.Curated

    Phylogenomic databases

    eggNOGiENOG4108ZI0. Bacteria.
    COG0241. LUCA.
    HOGENOMiHOG000016501.
    InParanoidiP63228.
    KOiK03273.
    OMAiSFMIGDK.
    PhylomeDBiP63228.

    Family and domain databases

    Gene3Di3.40.50.1000. 1 hit.
    InterProiIPR023214. HAD-like_dom.
    IPR006549. HAD-SF_hydro_IIIA.
    IPR004446. Heptose_bisP_phosphatase.
    IPR006543. Histidinol-phos.
    [Graphical view]
    PIRSFiPIRSF004682. GmhB. 1 hit.
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR00213. GmhB_yaeD. 1 hit.
    TIGR01662. HAD-SF-IIIA. 1 hit.
    TIGR01656. Histidinol-ppas. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P63228-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAKSVPAIFL DRDGTINVDH GYVHEIDNFE FIDGVIDAMR ELKKMGFALV
    60 70 80 90 100
    VVTNQSGIAR GKFTEAQFET LTEWMDWSLA DRDVDLDGIY YCPHHPQGSV
    110 120 130 140 150
    EEFRQVCDCR KPHPGMLLSA RDYLHIDMAA SYMVGDKLED MQAAVAANVG
    160 170 180 190
    TKVLVRTGKP ITPEAENAAD WVLNSLADLP QAIKKQQKPA Q
    Length:191
    Mass (Da):21,294
    Last modified:September 27, 2004 - v1
    Checksum:iE7814B34A23128FA
    GO

    Sequence cautioni

    The sequence BAA03661 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D15061 Genomic DNA. Translation: BAA03661.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73311.1.
    AP009048 Genomic DNA. Translation: BAA77877.1.
    U70214 Genomic DNA. Translation: AAB08628.1.
    PIRiH64744.
    RefSeqiNP_414742.1. NC_000913.3.
    WP_001140187.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73311; AAC73311; b0200.
    BAA77877; BAA77877; BAA77877.
    GeneIDi944879.
    KEGGiecj:JW0196.
    eco:b0200.
    PATRICi32115513. VBIEscCol129921_0208.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D15061 Genomic DNA. Translation: BAA03661.1. Different initiation.
    U00096 Genomic DNA. Translation: AAC73311.1.
    AP009048 Genomic DNA. Translation: BAA77877.1.
    U70214 Genomic DNA. Translation: AAB08628.1.
    PIRiH64744.
    RefSeqiNP_414742.1. NC_000913.3.
    WP_001140187.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2GMWX-ray1.50A/B1-191[»]
    3ESQX-ray1.70A1-191[»]
    3ESRX-ray1.95A1-191[»]
    3L1UX-ray1.95A/B1-191[»]
    3L1VX-ray1.95A/B1-191[»]
    3L8EX-ray1.64A/B1-187[»]
    3L8FX-ray1.79A1-187[»]
    3L8GX-ray2.18A1-187[»]
    ProteinModelPortaliP63228.
    SMRiP63228. Positions 4-187.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259752. 280 interactions.
    DIPiDIP-47998N.
    IntActiP63228. 11 interactions.
    STRINGi511145.b0200.

    Proteomic databases

    PaxDbiP63228.
    PRIDEiP63228.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73311; AAC73311; b0200.
    BAA77877; BAA77877; BAA77877.
    GeneIDi944879.
    KEGGiecj:JW0196.
    eco:b0200.
    PATRICi32115513. VBIEscCol129921_0208.

    Organism-specific databases

    EchoBASEiEB1687.
    EcoGeneiEG11736. gmhB.

    Phylogenomic databases

    eggNOGiENOG4108ZI0. Bacteria.
    COG0241. LUCA.
    HOGENOMiHOG000016501.
    InParanoidiP63228.
    KOiK03273.
    OMAiSFMIGDK.
    PhylomeDBiP63228.

    Enzyme and pathway databases

    UniPathwayiUPA00356; UER00438.
    UPA00958.
    BioCyciEcoCyc:EG11736-MONOMER.
    ECOL316407:JW0196-MONOMER.
    MetaCyc:EG11736-MONOMER.
    BRENDAi3.1.3.82. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP63228.
    PROiP63228.

    Family and domain databases

    Gene3Di3.40.50.1000. 1 hit.
    InterProiIPR023214. HAD-like_dom.
    IPR006549. HAD-SF_hydro_IIIA.
    IPR004446. Heptose_bisP_phosphatase.
    IPR006543. Histidinol-phos.
    [Graphical view]
    PIRSFiPIRSF004682. GmhB. 1 hit.
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR00213. GmhB_yaeD. 1 hit.
    TIGR01662. HAD-SF-IIIA. 1 hit.
    TIGR01656. Histidinol-ppas. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiGMHBB_ECOLI
    AccessioniPrimary (citable) accession number: P63228
    Secondary accession number(s): P31546
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 27, 2004
    Last sequence update: September 27, 2004
    Last modified: September 7, 2016
    This is version 103 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Phosphatase activity is essential for nucleotide activation (fourth step). Zinc ion does not directly participate in catalysis, but probably functions to stabilize the loop conformation.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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

    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 one 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.