HYPB_ECOLI
ID HYPB_ECOLI Reviewed; 290 AA.
AC P0AAN3; P24190; Q2MAA2; Q46884;
DT 11-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 11-OCT-2005, sequence version 1.
DT 03-AUG-2022, entry version 110.
DE RecName: Full=Hydrogenase maturation factor HypB {ECO:0000305};
DE AltName: Full=Hydrogenase isoenzymes nickel incorporation protein HypB {ECO:0000305};
GN Name=hypB; OrderedLocusNames=b2727, JW2697;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1849603; DOI=10.1111/j.1365-2958.1991.tb01833.x;
RA Lutz S., Jacobi A., Schlensog V., Boehm R., Sawers G., Boeck A.;
RT "Molecular characterization of an operon (hyp) necessary for the activity
RT of the three hydrogenase isoenzymes in Escherichia coli.";
RL Mol. Microbiol. 5:123-135(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [4]
RP PROTEIN SEQUENCE OF 27-31; 40-46 AND 76-81, FUNCTION, AND MUTAGENESIS OF
RP LYS-117 AND ASP-241.
RX PubMed=7601092; DOI=10.1111/j.1432-1033.1995.tb20543.x;
RA Maier T., Lottspeich F., Bock A.;
RT "GTP hydrolysis by HypB is essential for nickel insertion into hydrogenases
RT of Escherichia coli.";
RL Eur. J. Biochem. 230:133-138(1995).
RN [5]
RP FUNCTION.
RC STRAIN=K12 / MC4100 / ATCC 35695 / DSM 6574;
RX PubMed=8756471; DOI=10.1021/bi960567l;
RA Maier T., Boeck A.;
RT "Generation of active [NiFe] hydrogenase in vitro from a nickel-free
RT precursor form.";
RL Biochemistry 35:10089-10093(1996).
RN [6]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [7]
RP DOMAIN, METAL-BINDING, AND MUTAGENESIS OF CYS-2; CYS-5; CYS-7; CYS-166;
RP HIS-167 AND CYS-198.
RX PubMed=16142921; DOI=10.1021/bi050993j;
RA Leach M.R., Sandal S., Sun H., Zamble D.B.;
RT "Metal binding activity of the Escherichia coli hydrogenase maturation
RT factor HypB.";
RL Biochemistry 44:12229-12238(2005).
RN [8]
RP INTERACTION WITH HYPA.
RX PubMed=15995183; DOI=10.1128/jb.187.14.4689-4697.2005;
RA Atanassova A., Zamble D.B.;
RT "Escherichia coli HypA is a zinc metalloprotein with a weak affinity for
RT nickel.";
RL J. Bacteriol. 187:4689-4697(2005).
RN [9]
RP INTERACTION WITH SLYD.
RX PubMed=15569666; DOI=10.1074/jbc.m411799200;
RA Zhang J.W., Butland G., Greenblatt J.F., Emili A., Zamble D.B.;
RT "A role for SlyD in the Escherichia coli hydrogenase biosynthetic
RT pathway.";
RL J. Biol. Chem. 280:4360-4366(2005).
RN [10]
RP DOMAIN, METAL-BINDING, AND MUTAGENESIS OF CYS-7; CYS-166 AND HIS-167.
RX PubMed=18942856; DOI=10.1021/bi801337x;
RA Dias A.V., Mulvihill C.M., Leach M.R., Pickering I.J., George G.N.,
RA Zamble D.B.;
RT "Structural and biological analysis of the metal sites of Escherichia coli
RT hydrogenase accessory protein HypB.";
RL Biochemistry 47:11981-11991(2008).
RN [11]
RP FUNCTION, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND
RP MUTAGENESIS OF LEU-242 AND LEU-246.
RX PubMed=21544686; DOI=10.1007/s00775-011-0782-y;
RA Cai F., Ngu T.T., Kaluarachchi H., Zamble D.B.;
RT "Relationship between the GTPase, metal-binding, and dimerization
RT activities of E. coli HypB.";
RL J. Biol. Inorg. Chem. 16:857-868(2011).
RN [12]
RP FUNCTION, INTERACTION WITH HYPA, AND MUTAGENESIS OF 78-LEU--VAL-80.
RX PubMed=23899293; DOI=10.1021/bi400812r;
RA Douglas C.D., Ngu T.T., Kaluarachchi H., Zamble D.B.;
RT "Metal transfer within the Escherichia coli HypB-HypA complex of
RT hydrogenase accessory proteins.";
RL Biochemistry 52:6030-6039(2013).
RN [13]
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=27951644; DOI=10.1021/acs.biochem.6b00706;
RA Lacasse M.J., Douglas C.D., Zamble D.B.;
RT "Mechanism of selective nickel transfer from HypB to HypA, Escherichia coli
RT [NiFe]-hydrogenase accessory proteins.";
RL Biochemistry 55:6821-6831(2016).
CC -!- FUNCTION: Involved in the maturation of [NiFe] hydrogenases. Required
CC for nickel insertion into the metal center of the hydrogenase
CC (PubMed:7601092, PubMed:8756471). Exhibits a low intrinsic GTPase
CC activity, which is essential for nickel insertion (PubMed:7601092,
CC PubMed:21544686, PubMed:27951644). In the presence of GDP, nickel, but
CC not zinc, is transferred from the HypB GTPase domain (G-domain) to HypA
CC (PubMed:23899293, PubMed:27951644). {ECO:0000269|PubMed:21544686,
CC ECO:0000269|PubMed:23899293, ECO:0000269|PubMed:27951644,
CC ECO:0000269|PubMed:7601092, ECO:0000269|PubMed:8756471}.
CC -!- ACTIVITY REGULATION: Binding of zinc or nickel in the G-domain
CC decreases GTPase activity (PubMed:21544686). Once GTP hydrolysis is
CC triggered, probably via a GTPase activating protein, the GDP-loaded
CC state may enhance HypA-HypB complex formation and reduces the affinity
CC of HypB for nickel, which is then transferred to HypA
CC (PubMed:27951644). In contrast to nickel, zinc reduces the formation of
CC complexes with HypA (PubMed:27951644). {ECO:0000269|PubMed:21544686,
CC ECO:0000269|PubMed:27951644}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Note=kcat is 0.18 min(-1) for GTPase activity. kcat is 0.04 min(1)
CC for GTPase activity in the presence of 1 uM Zn(II). kcat is 0.10
CC min(-1) for GTPase activity in the presence of 10 uM Ni(II).
CC {ECO:0000269|PubMed:21544686};
CC -!- SUBUNIT: Monomer (PubMed:21544686). Can form homodimers, but
CC dimerization does not have a critical role in the hydrogenase
CC maturation pathway (PubMed:21544686). Forms complexes with HypA and
CC SlyD (PubMed:15995183, PubMed:15569666, PubMed:23899293).
CC {ECO:0000269|PubMed:15569666, ECO:0000269|PubMed:15995183,
CC ECO:0000269|PubMed:21544686, ECO:0000269|PubMed:23899293}.
CC -!- INTERACTION:
CC P0AAN3; P0A700: hypA; NbExp=9; IntAct=EBI-558261, EBI-6290024;
CC P0AAN3; P0A9K9: slyD; NbExp=6; IntAct=EBI-558261, EBI-369251;
CC -!- DOMAIN: The N-terminal region contains a high-affinity nickel-binding
CC site and the C-terminal G-domain contains a low-affinity metal-binding
CC site, which is not selective for nickel and could possibly accommodate
CC other divalent metals (PubMed:16142921, PubMed:18942856). Both metal
CC sites are critical for the maturation of the hydrogenases
CC (PubMed:18942856). {ECO:0000269|PubMed:16142921,
CC ECO:0000269|PubMed:18942856}.
CC -!- SIMILARITY: Belongs to the SIMIBI class G3E GTPase family. HypB/HupM
CC subfamily. {ECO:0000305}.
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DR EMBL; X54543; CAA38413.1; -; Genomic_DNA.
DR EMBL; U29579; AAA69237.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75769.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76804.1; -; Genomic_DNA.
DR PIR; C65053; C65053.
DR RefSeq; NP_417207.1; NC_000913.3.
DR RefSeq; WP_000337665.1; NZ_SSUR01000024.1.
DR AlphaFoldDB; P0AAN3; -.
DR SMR; P0AAN3; -.
DR BioGRID; 4261427; 13.
DR ComplexPortal; CPX-5056; HypAB Ni-hydrogenase maturation complex.
DR DIP; DIP-36428N; -.
DR IntAct; P0AAN3; 9.
DR MINT; P0AAN3; -.
DR STRING; 511145.b2727; -.
DR SWISS-2DPAGE; P0AAN3; -.
DR jPOST; P0AAN3; -.
DR PaxDb; P0AAN3; -.
DR PRIDE; P0AAN3; -.
DR EnsemblBacteria; AAC75769; AAC75769; b2727.
DR EnsemblBacteria; BAE76804; BAE76804; BAE76804.
DR GeneID; 66673404; -.
DR GeneID; 947194; -.
DR KEGG; ecj:JW2697; -.
DR KEGG; eco:b2727; -.
DR PATRIC; fig|1411691.4.peg.4014; -.
DR EchoBASE; EB0479; -.
DR eggNOG; COG0378; Bacteria.
DR HOGENOM; CLU_056148_1_0_6; -.
DR InParanoid; P0AAN3; -.
DR OMA; ECHLDAH; -.
DR PhylomeDB; P0AAN3; -.
DR BioCyc; EcoCyc:EG10484-MON; -.
DR BioCyc; MetaCyc:EG10484-MON; -.
DR PRO; PR:P0AAN3; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:1905360; C:GTPase complex; IPI:ComplexPortal.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003924; F:GTPase activity; IDA:EcoCyc.
DR GO; GO:0016151; F:nickel cation binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0051604; P:protein maturation; IBA:GO_Central.
DR GO; GO:0110147; P:protein maturation by nickel ion transfer; IMP:EcoCyc.
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 Direct protein sequencing; GTP-binding; Hydrolase; Metal-binding; Nickel;
KW Nucleotide-binding; Reference proteome; Zinc.
FT CHAIN 1..290
FT /note="Hydrogenase maturation factor HypB"
FT /id="PRO_0000201440"
FT REGION 106..267
FT /note="G-domain"
FT /evidence="ECO:0000305"
FT BINDING 2
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="1"
FT /evidence="ECO:0000305|PubMed:16142921,
FT ECO:0000305|PubMed:18942856"
FT BINDING 5
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="1"
FT /evidence="ECO:0000305|PubMed:16142921,
FT ECO:0000305|PubMed:18942856"
FT BINDING 7
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="1"
FT /evidence="ECO:0000305|PubMed:16142921,
FT ECO:0000305|PubMed:18942856"
FT BINDING 166
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:16142921,
FT ECO:0000305|PubMed:18942856"
FT BINDING 166
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:16142921,
FT ECO:0000305|PubMed:18942856"
FT BINDING 167
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:16142921,
FT ECO:0000305|PubMed:18942856"
FT BINDING 167
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:16142921,
FT ECO:0000305|PubMed:18942856"
FT BINDING 198
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT /ligand_label="2"
FT /evidence="ECO:0000305|PubMed:16142921"
FT BINDING 198
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000305|PubMed:16142921"
FT MUTAGEN 2
FT /note="C->A: Decreases nickel content. Disruption of the N-
FT terminal metal-binding site; when associated with A-5 and
FT A-7."
FT /evidence="ECO:0000269|PubMed:16142921"
FT MUTAGEN 5
FT /note="C->A: Decreases nickel content. Disruption of the N-
FT terminal metal-binding site; when associated with A-3 and
FT A-7."
FT /evidence="ECO:0000269|PubMed:16142921"
FT MUTAGEN 7
FT /note="C->A: Decreases nickel content. Decreases
FT hydrogenase activity of the cell. Disruption of the N-
FT terminal metal-binding site; when associated with A-3 and
FT A-5."
FT /evidence="ECO:0000269|PubMed:16142921,
FT ECO:0000269|PubMed:18942856"
FT MUTAGEN 78..80
FT /note="LEV->AEA: Disrupts interaction with HypA. Can only
FT partially restore hydrogenase production in a hypB deletion
FT mutant."
FT /evidence="ECO:0000269|PubMed:23899293"
FT MUTAGEN 117
FT /note="K->N: Important decrease in GTPase activity."
FT /evidence="ECO:0000269|PubMed:7601092"
FT MUTAGEN 166
FT /note="C->A: Does not affect nickel content. Mutant lacks
FT hydrogenase activity."
FT /evidence="ECO:0000269|PubMed:16142921,
FT ECO:0000269|PubMed:18942856"
FT MUTAGEN 167
FT /note="H->A: Does not affect nickel content. Mutant lacks
FT hydrogenase activity."
FT /evidence="ECO:0000269|PubMed:16142921,
FT ECO:0000269|PubMed:18942856"
FT MUTAGEN 198
FT /note="C->A: Does not affect nickel content."
FT /evidence="ECO:0000269|PubMed:16142921"
FT MUTAGEN 241
FT /note="D->N: 85-fold decrease in kcat/KM value of GTPase
FT activity and loss of the specificity for GTP."
FT /evidence="ECO:0000269|PubMed:7601092"
FT MUTAGEN 242
FT /note="L->A: Cannot form dimers. Can still bind metal in
FT both sites and activate GTP hydrolysis, but hydrogenase
FT activity of the cell is decreased; when associated with A-
FT 246."
FT /evidence="ECO:0000269|PubMed:21544686"
FT MUTAGEN 246
FT /note="L->A: Cannot form dimers. Can still bind metal in
FT both sites and activate GTP hydrolysis, but hydrogenase
FT activity of the cell is decreased; when associated with A-
FT 242."
FT /evidence="ECO:0000269|PubMed:21544686"
FT CONFLICT 36
FT /note="P -> R (in Ref. 1; CAA38413)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 290 AA; 31565 MW; 5B3AEB59AA6915C3 CRC64;
MCTTCGCGEG NLYIEGDEHN PHSAFRSAPF APAARPKMKI TGIKAPEFTP SQTEEGDLHY
GHGEAGTHAP GMSQRRMLEV EIDVLDKNNR LAERNRARFA ARKQLVLNLV SSPGSGKTTL
LTETLMRLKD SVPCAVIEGD QQTVNDAARI RATGTPAIQV NTGKGCHLDA QMIADAAPRL
PLDDNGILFI ENVGNLVCPA SFDLGEKHKV AVLSVTEGED KPLKYPHMFA AASLMLLNKV
DLLPYLNFDV EKCIACAREV NPEIEIILIS ATSGEGMDQW LNWLETQRCA
