Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

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

Gene

gmhB

Organism
Rhizobium loti (strain MAFF303099) (Mesorhizobium loti)
Status
Reviewed-Annotation score: Annotation score: 4 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.1 Publication

Catalytic activityi

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

Cofactori

Mg2+By similarity

Kineticsi

kcat is 18 sec(-1) and 4.4 sec(-1) with beta-HBP and alpha-HBP as substrate, respectively. Thus, the enzyme displays 18-fold more efficiency towards the beta- than the alpha-anomer (PubMed:20050615).1 Publication

  1. KM=13 µM for beta-HBP (at pH 7.5 and 25 degrees Celsius)1 Publication
  2. KM=58 µM for alpha-HBP (at pH 7.5 and 25 degrees Celsius)1 Publication

    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.
    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.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei36 – 361NucleophileBy similarity
    Metal bindingi36 – 361MagnesiumBy similarity
    Active sitei38 – 381Proton donorBy similarity
    Metal bindingi38 – 381Magnesium; via carbonyl oxygenBy similarity
    Sitei78 – 781Stabilizes the phosphoryl groupBy similarity
    Sitei135 – 1351Contributes to substrate recognitionBy similarity
    Sitei136 – 1361Stabilizes the phosphoryl groupBy similarity
    Metal bindingi161 – 1611MagnesiumBy similarity
    Metal bindingi162 – 1621MagnesiumBy similarity
    Binding sitei162 – 1621SubstrateBy similarity

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Carbohydrate metabolism

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMLOT266835:GJ9L-1998-MONOMER.
    BRENDAi3.1.3.82. 3243.
    UniPathwayiUPA00356; UER00438.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase (EC:3.1.3.82)
    Alternative name(s):
    D,D-heptose 1,7-bisphosphate phosphatase
    Short name:
    HBP phosphatase
    Gene namesi
    Name:gmhB
    Ordered Locus Names:mll2559
    OrganismiRhizobium loti (strain MAFF303099) (Mesorhizobium loti)
    Taxonomic identifieri266835 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesPhyllobacteriaceaeMesorhizobium
    Proteomesi
    • UP000000552 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 217217D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatasePRO_0000424236Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.By similarity

    Protein-protein interaction databases

    STRINGi266835.mll2559.

    Structurei

    Secondary structure

    1
    217
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi11 – 133Combined sources
    Beta strandi16 – 205Combined sources
    Beta strandi33 – 353Combined sources
    Turni39 – 413Combined sources
    Helixi51 – 533Combined sources
    Helixi58 – 603Combined sources
    Helixi61 – 7010Combined sources
    Beta strandi74 – 796Combined sources
    Helixi81 – 844Combined sources
    Helixi90 – 10617Combined sources
    Beta strandi112 – 1176Combined sources
    Helixi140 – 14910Combined sources
    Helixi153 – 1553Combined sources
    Beta strandi157 – 1626Combined sources
    Helixi163 – 1719Combined sources
    Beta strandi175 – 1806Combined sources
    Beta strandi185 – 1873Combined sources
    Beta strandi190 – 1978Combined sources
    Helixi198 – 21013Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2O2XX-ray1.50A1-217[»]
    ProteinModelPortaliQ98I56.
    SMRiQ98I56. Positions 8-216.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ98I56.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni36 – 383Substrate bindingBy similarity
    Regioni44 – 474Substrate bindingBy similarity
    Regioni78 – 814Substrate bindingBy similarity
    Regioni135 – 1362Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the gmhB family.Curated

    Phylogenomic databases

    eggNOGiENOG4108ZI0. Bacteria.
    COG0241. LUCA.
    HOGENOMiHOG000016501.
    KOiK03273.
    OMAiVLACAYH.
    OrthoDBiEOG6QG8GT.

    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.
    TIGRFAMsiTIGR01662. HAD-SF-IIIA. 1 hit.
    TIGR01656. Histidinol-ppas. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q98I56-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MADKTGTPHP LTEPGVWIER IGGRVFPPHL PALFLDRDGT INVDTDYPSD
    60 70 80 90 100
    PAEIVLRPQM LPAIATANRA GIPVVVVTNQ SGIARGYFGW SAFAAVNGRV
    110 120 130 140 150
    LELLREEGVF VDMVLACAYH EAGVGPLAIP DHPMRKPNPG MLVEAGKRLA
    160 170 180 190 200
    LDLQRSLIVG DKLADMQAGK RAGLAQGWLV DGEAAVQPGF AIRPLRDSSE
    210
    LGDLLAAIET LGRDNRS
    Length:217
    Mass (Da):23,200
    Last modified:October 1, 2001 - v1
    Checksum:i7BC2E4C716063DE7
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000012 Genomic DNA. Translation: BAB49660.1.
    RefSeqiWP_010911012.1. NC_002678.2.

    Genome annotation databases

    EnsemblBacteriaiBAB49660; BAB49660; BAB49660.
    GeneIDi1226535.
    KEGGimlo:mll2559.
    PATRICi22478295. VBIMesLot2464_2054.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000012 Genomic DNA. Translation: BAB49660.1.
    RefSeqiWP_010911012.1. NC_002678.2.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2O2XX-ray1.50A1-217[»]
    ProteinModelPortaliQ98I56.
    SMRiQ98I56. Positions 8-216.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi266835.mll2559.

    Protocols and materials databases

    DNASUi1226535.
    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAB49660; BAB49660; BAB49660.
    GeneIDi1226535.
    KEGGimlo:mll2559.
    PATRICi22478295. VBIMesLot2464_2054.

    Phylogenomic databases

    eggNOGiENOG4108ZI0. Bacteria.
    COG0241. LUCA.
    HOGENOMiHOG000016501.
    KOiK03273.
    OMAiVLACAYH.
    OrthoDBiEOG6QG8GT.

    Enzyme and pathway databases

    UniPathwayiUPA00356; UER00438.
    BioCyciMLOT266835:GJ9L-1998-MONOMER.
    BRENDAi3.1.3.82. 3243.

    Miscellaneous databases

    EvolutionaryTraceiQ98I56.

    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.
    TIGRFAMsiTIGR01662. HAD-SF-IIIA. 1 hit.
    TIGR01656. Histidinol-ppas. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: MAFF303099.
    2. "Divergence of biochemical function in the HAD superfamily: D-glycero-D-manno-heptose-1,7-bisphosphate phosphatase (GmhB)."
      Wang L., Huang H., Nguyen H.H., Allen K.N., Mariano P.S., Dunaway-Mariano D.
      Biochemistry 49:1072-1081(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS.
    3. "Crystal structure of hypothetical protein (NP_103874.1) from Mesorhizobium loti at 1.50 A resolution."
      Joint Center for Structural Genomics (JCSG)
      Submitted (JUL-2011) to the PDB data bank
      Cited for: X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS).

    Entry informationi

    Entry nameiGMHBB_RHILO
    AccessioniPrimary (citable) accession number: Q98I56
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 16, 2013
    Last sequence update: October 1, 2001
    Last modified: November 11, 2015
    This is version 98 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.