HYPD_ECOLI
ID HYPD_ECOLI Reviewed; 373 AA.
AC P24192; Q2MAA0; Q46885;
DT 01-MAR-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-1992, sequence version 1.
DT 03-AUG-2022, entry version 146.
DE RecName: Full=Hydrogenase maturation factor HypD {ECO:0000305};
DE AltName: Full=Hydrogenase isoenzymes formation protein HypD {ECO:0000305};
GN Name=hypD {ECO:0000303|PubMed:1849603}; OrderedLocusNames=b2729, JW2699;
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 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 [5]
RP INTERACTION WITH HYPC.
RX PubMed=12441107; DOI=10.1016/s0022-2836(02)01070-7;
RA Blokesch M., Boeck A.;
RT "Maturation of [NiFe]-hydrogenases in Escherichia coli: the HypC cycle.";
RL J. Mol. Biol. 324:287-296(2002).
RN [6]
RP FUNCTION, COFACTOR, SUBUNIT, AND INTERACTION WITH HYPC AND HYPE.
RX PubMed=15504408; DOI=10.1016/j.jmb.2004.09.040;
RA Blokesch M., Albracht S.P., Matzanke B.F., Drapal N.M., Jacobi A.,
RA Boeck A.;
RT "The complex between hydrogenase-maturation proteins HypC and HypD is an
RT intermediate in the supply of cyanide to the active site iron of [NiFe]-
RT hydrogenases.";
RL J. Mol. Biol. 344:155-167(2004).
RN [7]
RP INTERACTION WITH HYBG AND HYPE.
RX PubMed=16412426; DOI=10.1016/j.febslet.2005.12.063;
RA Butland G., Zhang J.W., Yang W., Sheung A., Wong P., Greenblatt J.F.,
RA Emili A., Zamble D.B.;
RT "Interactions of the Escherichia coli hydrogenase biosynthetic proteins:
RT HybG complex formation.";
RL FEBS Lett. 580:677-681(2006).
RN [8]
RP FUNCTION, COFACTOR, INTERACTION WITH HYPC, AND MUTAGENESIS OF CYS-41.
RX PubMed=23022438; DOI=10.1016/j.febslet.2012.09.019;
RA Soboh B., Stripp S.T., Muhr E., Granich C., Braussemann M., Herzberg M.,
RA Heberle J., Gary Sawers R.;
RT "[NiFe]-hydrogenase maturation: isolation of a HypC-HypD complex carrying
RT diatomic CO and CN- ligands.";
RL FEBS Lett. 586:3882-3887(2012).
RN [9]
RP FUNCTION, IRON-BINDING, AND MUTAGENESIS OF CYS-41; CYS-69; CYS-72 AND
RP GLU-357.
RX PubMed=23597401; DOI=10.1021/bi400302v;
RA Stripp S.T., Soboh B., Lindenstrauss U., Braussemann M., Herzberg M.,
RA Nies D.H., Sawers R.G., Heberle J.;
RT "HypD is the scaffold protein for Fe-(CN)2CO cofactor assembly in [NiFe]-
RT hydrogenase maturation.";
RL Biochemistry 52:3289-3296(2013).
CC -!- FUNCTION: Involved in the maturation of [NiFe] hydrogenases. Involved
CC in the biosynthesis of the Fe(CN)(2)CO cofactor (PubMed:15504408,
CC PubMed:23022438). HypD may act as a scaffold on which the Fe(CN)(2)CO
CC cofactor is formed (PubMed:23597401). In complex with HypC, accepts the
CC cyanide ligand generated by HypF and HypE, and also coordinates the
CC carbon monoxide ligand (PubMed:15504408, PubMed:23022438). Required for
CC the formation of all three hydrogenase isoenzymes (Probable).
CC {ECO:0000269|PubMed:15504408, ECO:0000269|PubMed:23022438,
CC ECO:0000269|PubMed:23597401, ECO:0000305}.
CC -!- COFACTOR:
CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883;
CC Evidence={ECO:0000269|PubMed:15504408, ECO:0000269|PubMed:23022438};
CC -!- PATHWAY: Protein modification; [NiFe] hydrogenase maturation.
CC {ECO:0000305}.
CC -!- SUBUNIT: Monomer (PubMed:15504408). Interacts with HypC
CC (PubMed:12441107, PubMed:15504408, PubMed:23022438). Forms a complex
CC with HypC, or HybG, and HypE (PubMed:15504408, PubMed:16412426).
CC {ECO:0000269|PubMed:12441107, ECO:0000269|PubMed:15504408,
CC ECO:0000269|PubMed:16412426, ECO:0000269|PubMed:23022438}.
CC -!- INTERACTION:
CC P24192; P0AAM7: hybG; NbExp=7; IntAct=EBI-552711, EBI-562426;
CC -!- DOMAIN: In addition to the iron-sulfur cluster, contains two additional
CC oxygen-labile iron ions. {ECO:0000269|PubMed:23022438}.
CC -!- SIMILARITY: Belongs to the HypD family. {ECO:0000305}.
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DR EMBL; X54543; CAA38415.1; -; Genomic_DNA.
DR EMBL; U29579; AAA69239.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75771.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76806.1; -; Genomic_DNA.
DR PIR; S15200; S15200.
DR RefSeq; NP_417209.1; NC_000913.3.
DR RefSeq; WP_001212985.1; NZ_LN832404.1.
DR AlphaFoldDB; P24192; -.
DR SMR; P24192; -.
DR BioGRID; 4261425; 34.
DR BioGRID; 851521; 1.
DR ComplexPortal; CPX-5283; Hybg-HypDE Ni-hydrogenase maturation complex.
DR ComplexPortal; CPX-5284; HypCDE Ni-hydrogenase maturation complex.
DR DIP; DIP-9998N; -.
DR IntAct; P24192; 12.
DR STRING; 511145.b2729; -.
DR SWISS-2DPAGE; P24192; -.
DR jPOST; P24192; -.
DR PaxDb; P24192; -.
DR PRIDE; P24192; -.
DR EnsemblBacteria; AAC75771; AAC75771; b2729.
DR EnsemblBacteria; BAE76806; BAE76806; BAE76806.
DR GeneID; 947189; -.
DR KEGG; ecj:JW2699; -.
DR KEGG; eco:b2729; -.
DR PATRIC; fig|1411691.4.peg.4012; -.
DR EchoBASE; EB0481; -.
DR eggNOG; COG0409; Bacteria.
DR HOGENOM; CLU_048562_1_0_6; -.
DR InParanoid; P24192; -.
DR OMA; HVCGSHE; -.
DR PhylomeDB; P24192; -.
DR BioCyc; EcoCyc:EG10486-MON; -.
DR BioCyc; MetaCyc:EG10486-MON; -.
DR UniPathway; UPA00335; -.
DR PRO; PR:P24192; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IDA:EcoCyc.
DR GO; GO:0016887; F:ATP hydrolysis activity; IDA:EcoCyc.
DR GO; GO:0070025; F:carbon monoxide binding; IDA:EcoCyc.
DR GO; GO:0005506; F:iron ion binding; IDA:EcoCyc.
DR GO; GO:0051604; P:protein maturation; IMP:EcoCyc.
DR Gene3D; 3.40.50.11740; -; 2.
DR Gene3D; 6.10.20.100; -; 1.
DR InterPro; IPR002780; Hyd_form_HypD.
DR InterPro; IPR042243; HypD_1.
DR InterPro; IPR042244; HypD_2_sf.
DR PANTHER; PTHR30149; PTHR30149; 1.
DR Pfam; PF01924; HypD; 1.
DR PIRSF; PIRSF005622; Hydrgn_mat_hypD; 1.
DR TIGRFAMs; TIGR00075; hypD; 1.
PE 1: Evidence at protein level;
KW 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Reference proteome.
FT CHAIN 1..373
FT /note="Hydrogenase maturation factor HypD"
FT /id="PRO_0000201451"
FT BINDING 41
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000305|PubMed:23597401"
FT BINDING 69
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000305|PubMed:23022438,
FT ECO:0000305|PubMed:23597401"
FT BINDING 72
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /evidence="ECO:0000305|PubMed:23022438,
FT ECO:0000305|PubMed:23597401"
FT MUTAGEN 41
FT /note="C->A: Does not affect interaction with HypC. Retains
FT the 4Fe-4S cluster, but has less iron than the native
FT complex. Can no longer coordinate CN(-1) and CO."
FT /evidence="ECO:0000269|PubMed:23022438,
FT ECO:0000269|PubMed:23597401"
FT MUTAGEN 69
FT /note="C->A: Can no longer coordinate CN(-1) and CO.
FT Reduces iron content."
FT /evidence="ECO:0000269|PubMed:23597401"
FT MUTAGEN 72
FT /note="C->A: Can no longer coordinate CN(-1) and CO.
FT Reduces iron content."
FT /evidence="ECO:0000269|PubMed:23597401"
FT MUTAGEN 357
FT /note="E->A,D: Does not affect CN(-1) and CO coordination."
FT /evidence="ECO:0000269|PubMed:23597401"
SQ SEQUENCE 373 AA; 41363 MW; 0E4186081FAA4C54 CRC64;
MRFVDEYRAP EQVMQLIEHL RERASHLSYT AERPLRIMEV CGGHTHAIFK FGLDQLLPEN
VEFIHGPGCP VCVLPMGRID TCVEIASHPE VIFCTFGDAM RVPGKQGSLL QAKARGADVR
IVYSPMDALK LAQENPTRKV VFFGLGFETT MPTTAITLQQ AKARDVQNFY FFCQHITLIP
TLRSLLEQPD NGIDAFLAPG HVSMVIGTDA YNFIASDFHR PLVVAGFEPL DLLQGVVMLV
QQKIAAHSKV ENQYRRVVPD AGNLLAQQAI ADVFCVNGDS EWRGLGVIES SGVHLTPDYQ
RFDAEAHFRP APQQVCDDPR ARCGEVLTGK CKPHQCPLFG NTCNPQTAFG ALMVSSEGAC
AAWYQYRQQE SEA
