HYPB_HELPY
ID HYPB_HELPY Reviewed; 242 AA.
AC O25560;
DT 01-JUN-2001, integrated into UniProtKB/Swiss-Prot.
DT 01-JAN-1998, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Hydrogenase/urease maturation factor HypB {ECO:0000305};
DE AltName: Full=Hydrogenase/urease nickel incorporation protein HypB {ECO:0000305};
GN Name=hypB; OrderedLocusNames=HP_0900;
OS Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=85962;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=9252185; DOI=10.1038/41483;
RA Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT "The complete genome sequence of the gastric pathogen Helicobacter
RT pylori.";
RL Nature 388:539-547(1997).
RN [2]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 43504 / NCTC 11637 / JCM 7653 / RPH 13487;
RX PubMed=11123699; DOI=10.1046/j.1365-2958.2001.02244.x;
RA Olson J.W., Mehta N.S., Maier R.J.;
RT "Requirement of nickel metabolism proteins HypA and HypB for full activity
RT of both hydrogenase and urease in Helicobacter pylori.";
RL Mol. Microbiol. 39:176-182(2001).
RN [3]
RP FUNCTION, SUBUNIT, INTERACTION WITH HYPA, AND MUTAGENESIS OF LYS-59.
RC STRAIN=ATCC 43504;
RX PubMed=12533448; DOI=10.1128/jb.185.3.726-734.2003;
RA Mehta N., Olson J.W., Maier R.J.;
RT "Characterization of Helicobacter pylori nickel metabolism accessory
RT proteins needed for maturation of both urease and hydrogenase.";
RL J. Bacteriol. 185:726-734(2003).
RN [4]
RP MUTAGENESIS OF LYS-59.
RC STRAIN=ATCC 43504 / NCTC 11637 / JCM 7653 / RPH 13487;
RX PubMed=14521881; DOI=10.1016/s0882-4010(03)00151-7;
RA Mehta N., Benoit S., Maier R.J.;
RT "Roles of conserved nucleotide-binding domains in accessory proteins, HypB
RT and UreG, in the maturation of nickel-enzymes required for efficient
RT Helicobacter pylori colonization.";
RL Microb. Pathog. 35:229-234(2003).
RN [5]
RP FUNCTION, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP DOMAIN, NICKEL-BINDING, ZINC-BINDING, AND MUTAGENESIS OF 106-CYS-HIS-107.
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=21239585; DOI=10.1128/jb.01333-10;
RA Sydor A.M., Liu J., Zamble D.B.;
RT "Effects of metal on the biochemical properties of Helicobacter pylori
RT HypB, a maturation factor of [NiFe]-hydrogenase and urease.";
RL J. Bacteriol. 193:1359-1368(2011).
RN [6]
RP FUNCTION, SUBUNIT, INTERACTION WITH HYPA, AND MUTAGENESIS OF LYS-18;
RP VAL-20; LYS-21; ILE-22; LYS-168; MET-186 AND PHE-190.
RC STRAIN=ATCC 700392 / 26695;
RX PubMed=22179820; DOI=10.1074/jbc.m111.287581;
RA Xia W., Li H., Yang X., Wong K.B., Sun H.;
RT "Metallo-GTPase HypB from Helicobacter pylori and its interaction with
RT nickel chaperone protein HypA.";
RL J. Biol. Chem. 287:6753-6763(2012).
RN [7] {ECO:0007744|PDB:4LPS}
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH NICKEL, FUNCTION,
RP ACTIVITY REGULATION, SUBUNIT, DOMAIN, AND MUTAGENESIS OF HIS-107 AND
RP CYS-142.
RX PubMed=24338018; DOI=10.1074/jbc.m113.502781;
RA Sydor A.M., Lebrette H., Ariyakumaran R., Cavazza C., Zamble D.B.;
RT "Relationship between Ni(II) and Zn(II) coordination and nucleotide binding
RT by the Helicobacter pylori [NiFe]-hydrogenase and urease maturation factor
RT HypB.";
RL J. Biol. Chem. 289:3828-3841(2014).
CC -!- FUNCTION: Involved in the maturation of [NiFe] hydrogenases. Required
CC for nickel insertion into the metal center of the hydrogenase. Is also
CC required for maturation of urease (PubMed:11123699, PubMed:12533448).
CC Exhibits a low intrinsic GTPase activity, which is essential for nickel
CC insertion (PubMed:12533448, PubMed:21239585, PubMed:22179820,
CC PubMed:24338018). {ECO:0000269|PubMed:12533448,
CC ECO:0000269|PubMed:21239585, ECO:0000269|PubMed:22179820,
CC ECO:0000269|PubMed:24338018, ECO:0000305|PubMed:11123699,
CC ECO:0000305|PubMed:12533448}.
CC -!- ACTIVITY REGULATION: Metal coordination and the nucleotide-bound state
CC of HypB directly influence each other (PubMed:24338018). Binding of
CC nickel in the G-domain decreases GTPase activity and modulates the
CC oligomeric state of the protein (PubMed:21239585, PubMed:24338018).
CC Binding of zinc inhibits the GTPase activity (PubMed:21239585,
CC PubMed:24338018). GTP and GDP modulate coordination, stoichiometry, and
CC affinity of nickel, but not zinc (PubMed:24338018). Potassium increases
CC the GTPase activity but has no effect on the other biochemical
CC properties of the protein (PubMed:24338018).
CC {ECO:0000269|PubMed:21239585, ECO:0000269|PubMed:24338018}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.05 mM for GTP (apo form) {ECO:0000269|PubMed:21239585};
CC KM=0.16 mM for GTP (in the presence of 20 uM Ni(II))
CC {ECO:0000269|PubMed:21239585};
CC Note=kcat is 0.0006 sec(-1) for the apo form. kcat is 0.0016 sec(-1)
CC in the presence of 20 uM Ni(II). {ECO:0000269|PubMed:21239585};
CC -!- SUBUNIT: Monomer and homodimer (PubMed:12533448, PubMed:24338018,
CC PubMed:21239585, PubMed:22179820). Dimerization is induced by nickel,
CC but not by zinc (PubMed:21239585). Dimerization is also induced by GTP
CC (PubMed:22179820). Forms complexes with HypA (PubMed:12533448,
CC PubMed:22179820). {ECO:0000269|PubMed:12533448,
CC ECO:0000269|PubMed:21239585, ECO:0000269|PubMed:22179820,
CC ECO:0000269|PubMed:24338018}.
CC -!- DOMAIN: Contains a metal-binding site, which can bind nickel or zinc,
CC with a higher affinity for zinc (PubMed:21239585). His-107 is an
CC essential nickel ligand only in the nucleotide-free state of the
CC protein (PubMed:24338018). {ECO:0000269|PubMed:21239585,
CC ECO:0000269|PubMed:24338018}.
CC -!- DISRUPTION PHENOTYPE: Mutant has negligible hydrogenase activity and is
CC severely impaired in urease activity. {ECO:0000269|PubMed:11123699}.
CC -!- SIMILARITY: Belongs to the SIMIBI class G3E GTPase family. HypB/HupM
CC subfamily. {ECO:0000305}.
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DR EMBL; AE000511; AAD07946.1; -; Genomic_DNA.
DR PIR; D64632; D64632.
DR RefSeq; NP_207693.1; NC_000915.1.
DR RefSeq; WP_000003622.1; NC_018939.1.
DR PDB; 4LPS; X-ray; 2.00 A; A/B=1-242.
DR PDBsum; 4LPS; -.
DR AlphaFoldDB; O25560; -.
DR SMR; O25560; -.
DR DIP; DIP-3235N; -.
DR IntAct; O25560; 2.
DR MINT; O25560; -.
DR STRING; 85962.C694_04620; -.
DR PaxDb; O25560; -.
DR PRIDE; O25560; -.
DR EnsemblBacteria; AAD07946; AAD07946; HP_0900.
DR KEGG; hpy:HP_0900; -.
DR PATRIC; fig|85962.47.peg.959; -.
DR eggNOG; COG0378; Bacteria.
DR OMA; ECHLDAH; -.
DR PhylomeDB; O25560; -.
DR BioCyc; MetaCyc:HP_RS04400-MON; -.
DR Proteomes; UP000000429; Chromosome.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003924; F:GTPase activity; IBA:GO_Central.
DR GO; GO:0016151; F:nickel cation binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR GO; GO:0051604; P:protein maturation; IBA:GO_Central.
DR CDD; cd05390; HypB; 1.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR003495; CobW/HypB/UreG_dom.
DR InterPro; IPR004392; Hyd_mat_HypB.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR30134; PTHR30134; 1.
DR Pfam; PF02492; cobW; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00073; hypB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; GTP-binding; Hydrolase; Metal-binding; Nickel;
KW Nucleotide-binding; Reference proteome; Zinc.
FT CHAIN 1..242
FT /note="Hydrogenase/urease maturation factor HypB"
FT /id="PRO_0000201442"
FT REGION 48..211
FT /note="G-domain"
FT /evidence="ECO:0000250|UniProtKB:P0AAN3"
FT BINDING 106
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:24338018,
FT ECO:0000305|PubMed:21239585, ECO:0007744|PDB:4LPS"
FT BINDING 106
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:21239585"
FT BINDING 107
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000305|PubMed:21239585,
FT ECO:0000305|PubMed:24338018"
FT BINDING 142
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /evidence="ECO:0000269|PubMed:24338018,
FT ECO:0000305|PubMed:21239585, ECO:0007744|PDB:4LPS"
FT BINDING 142
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:21239585"
FT MUTAGEN 18
FT /note="K->A: Decreases interaction with HypA."
FT /evidence="ECO:0000269|PubMed:22179820"
FT MUTAGEN 20
FT /note="V->A: Decreases interaction with HypA."
FT /evidence="ECO:0000269|PubMed:22179820"
FT MUTAGEN 21
FT /note="K->A: Does not affect interaction with HypA."
FT /evidence="ECO:0000269|PubMed:22179820"
FT MUTAGEN 22
FT /note="I->A: Decreases interaction with HypA."
FT /evidence="ECO:0000269|PubMed:22179820"
FT MUTAGEN 59
FT /note="K->A: No hydrogenase activity, 1% urease activity.
FT Normal amounts of apo-urease and HypB protein are produced.
FT Hydrogenase activity is partially restored and urease
FT activity is fully restored by growth on 5 uM Ni(2+). Almost
FT loss of GTPase activity."
FT /evidence="ECO:0000269|PubMed:12533448,
FT ECO:0000269|PubMed:14521881"
FT MUTAGEN 106..107
FT /note="CH->AA: Abrogates nickel binding and weakens the
FT affinity for zinc. Cannot dimerize in the presence of
FT nickel."
FT /evidence="ECO:0000269|PubMed:21239585"
FT MUTAGEN 107
FT /note="H->A: Strong decrease in nickel affinity in the
FT absence of nucleotide."
FT /evidence="ECO:0000269|PubMed:24338018"
FT MUTAGEN 142
FT /note="C->S: Weakens metal binding and decouples the GTPase
FT and metal binding activities."
FT /evidence="ECO:0000269|PubMed:24338018"
FT MUTAGEN 168
FT /note="K->A: Abolishes GTP-dependent dimerization, but does
FT not affect nickel-dependent dimerization. Loss of GTPase
FT activity."
FT /evidence="ECO:0000269|PubMed:22179820"
FT MUTAGEN 186
FT /note="M->L: Strong decrease in GTP-dependent dimerization,
FT but does not affect nickel-dependent dimerization; when
FT associated with V-190."
FT /evidence="ECO:0000269|PubMed:22179820"
FT MUTAGEN 190
FT /note="F->V: Strong decrease in GTP-dependent dimerization,
FT but does not affect nickel-dependent dimerization; when
FT associated with L-186."
FT /evidence="ECO:0000269|PubMed:22179820"
FT HELIX 29..43
FT /evidence="ECO:0007829|PDB:4LPS"
FT STRAND 47..52
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 59..66
FT /evidence="ECO:0007829|PDB:4LPS"
FT STRAND 74..82
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 85..91
FT /evidence="ECO:0007829|PDB:4LPS"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:4LPS"
FT STRAND 97..101
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 110..122
FT /evidence="ECO:0007829|PDB:4LPS"
FT TURN 123..128
FT /evidence="ECO:0007829|PDB:4LPS"
FT STRAND 130..135
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 142..145
FT /evidence="ECO:0007829|PDB:4LPS"
FT STRAND 151..158
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 159..161
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 165..168
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 170..174
FT /evidence="ECO:0007829|PDB:4LPS"
FT STRAND 177..182
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 184..186
FT /evidence="ECO:0007829|PDB:4LPS"
FT TURN 187..191
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 194..204
FT /evidence="ECO:0007829|PDB:4LPS"
FT STRAND 210..212
FT /evidence="ECO:0007829|PDB:4LPS"
FT HELIX 218..234
FT /evidence="ECO:0007829|PDB:4LPS"
SQ SEQUENCE 242 AA; 27310 MW; 7C505390FB5C0142 CRC64;
MSEQRQESLQ NNPNLSKKDV KIVEKILSKN DIKAAEMKER YLKEGLYVLN FMSSPGSGKT
TMLENLADFK DFKFCVVEGD LQTNRDADRL RKKGVSAHQI TTGEACHLEA SMIEGAFDLL
KDEGALEKSD FLIIENVGNL VCPSSYNLGA AMNIVLLSVP EGDDKVLKYP TMFMCADAVI
ISKADMVEVF NFRVSQVKED MQKLKPEAPI FLMSSKDPKS LEDFKNFLLE KKRENYQSTH
SF
