GMHBB_RHILO
ID GMHBB_RHILO Reviewed; 217 AA.
AC Q98I56;
DT 16-OCT-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2001, sequence version 1.
DT 03-AUG-2022, entry version 126.
DE RecName: Full=D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-phosphatase;
DE EC=3.1.3.82;
DE AltName: Full=D,D-heptose 1,7-bisphosphate phosphatase;
DE Short=HBP phosphatase;
GN Name=gmhB; OrderedLocusNames=mll2559;
OS Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS (Mesorhizobium loti (strain MAFF 303099)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Phyllobacteriaceae; Mesorhizobium.
OX NCBI_TaxID=266835;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LMG 29417 / CECT 9101 / MAFF 303099;
RX PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA Tabata S.;
RT "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT Mesorhizobium loti.";
RL DNA Res. 7:331-338(2000).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, AND KINETIC
RP PARAMETERS.
RX PubMed=20050615; DOI=10.1021/bi902018y;
RA Wang L., Huang H., Nguyen H.H., Allen K.N., Mariano P.S.,
RA Dunaway-Mariano D.;
RT "Divergence of biochemical function in the HAD superfamily: D-glycero-D-
RT manno-heptose-1,7-bisphosphate phosphatase (GmhB).";
RL Biochemistry 49:1072-1081(2010).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS).
RG Joint Center for Structural Genomics (JCSG);
RT "Crystal structure of hypothetical protein (NP_103874.1) from Mesorhizobium
RT loti at 1.50 A resolution.";
RL Submitted (JUL-2011) to the PDB data bank.
CC -!- FUNCTION: Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate
CC (beta-HBP) intermediate into D-glycero-beta-D-manno-heptose 1-phosphate
CC by removing the phosphate group at the C-7 position.
CC {ECO:0000269|PubMed:20050615}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glycero-beta-D-manno-heptose 1,7-bisphosphate + H2O = D-
CC glycero-beta-D-manno-heptose 1-phosphate + phosphate;
CC Xref=Rhea:RHEA:28518, ChEBI:CHEBI:15377, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:60208, ChEBI:CHEBI:61593; EC=3.1.3.82;
CC Evidence={ECO:0000269|PubMed:20050615};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=13 uM for beta-HBP (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20050615};
CC KM=58 uM for alpha-HBP (at pH 7.5 and 25 degrees Celsius)
CC {ECO:0000269|PubMed:20050615};
CC Note=kcat is 18 sec(-1) and 4.4 sec(-1) with beta-HBP and alpha-HBP
CC as substrate, respectively. Thus, the enzyme displays 18-fold more
CC efficiency towards the beta- than the alpha-anomer (PubMed:20050615).
CC {ECO:0000269|PubMed:20050615};
CC -!- PATHWAY: Nucleotide-sugar biosynthesis; ADP-L-glycero-beta-D-manno-
CC heptose biosynthesis; ADP-L-glycero-beta-D-manno-heptose from D-
CC glycero-beta-D-manno-heptose 7-phosphate: step 2/4.
CC -!- SUBUNIT: Monomer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the gmhB family. {ECO:0000305}.
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DR EMBL; BA000012; BAB49660.1; -; Genomic_DNA.
DR RefSeq; WP_010911012.1; NC_002678.2.
DR PDB; 2O2X; X-ray; 1.50 A; A=1-217.
DR PDBsum; 2O2X; -.
DR AlphaFoldDB; Q98I56; -.
DR SMR; Q98I56; -.
DR STRING; 266835.14023053; -.
DR DNASU; 1226535; -.
DR EnsemblBacteria; BAB49660; BAB49660; BAB49660.
DR KEGG; mlo:mll2559; -.
DR PATRIC; fig|266835.9.peg.2054; -.
DR eggNOG; COG0241; Bacteria.
DR HOGENOM; CLU_085077_3_1_5; -.
DR OMA; DHPMRKP; -.
DR OrthoDB; 1472357at2; -.
DR BRENDA; 3.1.3.82; 3243.
DR UniPathway; UPA00356; UER00438.
DR EvolutionaryTrace; Q98I56; -.
DR Proteomes; UP000000552; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0034200; F:D,D-heptose 1,7-bisphosphate phosphatase activity; IEA:RHEA.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0097171; P:ADP-L-glycero-beta-D-manno-heptose biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.1000; -; 1.
DR InterPro; IPR036412; HAD-like_sf.
DR InterPro; IPR006549; HAD-SF_hydro_IIIA.
DR InterPro; IPR023214; HAD_sf.
DR InterPro; IPR004446; Heptose_bisP_phosphatase.
DR InterPro; IPR006543; Histidinol-phos.
DR PANTHER; PTHR42891; PTHR42891; 1.
DR PIRSF; PIRSF004682; GmhB; 1.
DR SUPFAM; SSF56784; SSF56784; 1.
DR TIGRFAMs; TIGR01662; HAD-SF-IIIA; 1.
DR TIGRFAMs; TIGR01656; Histidinol-ppas; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Cytoplasm; Hydrolase; Magnesium;
KW Metal-binding.
FT CHAIN 1..217
FT /note="D-glycero-beta-D-manno-heptose-1,7-bisphosphate 7-
FT phosphatase"
FT /id="PRO_0000424236"
FT ACT_SITE 36
FT /note="Nucleophile"
FT /evidence="ECO:0000250"
FT ACT_SITE 38
FT /note="Proton donor"
FT /evidence="ECO:0000250"
FT BINDING 36..38
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 36
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 38
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 44..47
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 78..81
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 135..136
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 161
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 162
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 162
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT SITE 78
FT /note="Stabilizes the phosphoryl group"
FT /evidence="ECO:0000250"
FT SITE 135
FT /note="Contributes to substrate recognition"
FT /evidence="ECO:0000250"
FT SITE 136
FT /note="Stabilizes the phosphoryl group"
FT /evidence="ECO:0000250"
FT STRAND 11..13
FT /evidence="ECO:0007829|PDB:2O2X"
FT STRAND 16..20
FT /evidence="ECO:0007829|PDB:2O2X"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:2O2X"
FT TURN 39..41
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 58..60
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 61..70
FT /evidence="ECO:0007829|PDB:2O2X"
FT STRAND 74..79
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 81..84
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 90..106
FT /evidence="ECO:0007829|PDB:2O2X"
FT STRAND 112..117
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 140..149
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 153..155
FT /evidence="ECO:0007829|PDB:2O2X"
FT STRAND 157..162
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 163..171
FT /evidence="ECO:0007829|PDB:2O2X"
FT STRAND 175..180
FT /evidence="ECO:0007829|PDB:2O2X"
FT STRAND 185..187
FT /evidence="ECO:0007829|PDB:2O2X"
FT STRAND 190..197
FT /evidence="ECO:0007829|PDB:2O2X"
FT HELIX 198..210
FT /evidence="ECO:0007829|PDB:2O2X"
SQ SEQUENCE 217 AA; 23200 MW; 7BC2E4C716063DE7 CRC64;
MADKTGTPHP LTEPGVWIER IGGRVFPPHL PALFLDRDGT INVDTDYPSD PAEIVLRPQM
LPAIATANRA GIPVVVVTNQ SGIARGYFGW SAFAAVNGRV LELLREEGVF VDMVLACAYH
EAGVGPLAIP DHPMRKPNPG MLVEAGKRLA LDLQRSLIVG DKLADMQAGK RAGLAQGWLV
DGEAAVQPGF AIRPLRDSSE LGDLLAAIET LGRDNRS
