HYBD_ECOLI
ID HYBD_ECOLI Reviewed; 164 AA.
AC P37182; Q2M9K2;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 2.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Hydrogenase 2 maturation protease;
DE EC=3.4.23.-;
GN Name=hybD; OrderedLocusNames=b2993, JW2961;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / TG1;
RX PubMed=8021226; DOI=10.1128/jb.176.14.4416-4423.1994;
RA Menon N.K., Chatelus C.Y., Dervartanian M., Wendt J.C., Shanmugam K.T.,
RA Peck H.D. Jr., Przybyla A.E.;
RT "Cloning, sequencing, and mutational analysis of the hyb operon encoding
RT Escherichia coli hydrogenase 2.";
RL J. Bacteriol. 176:4416-4423(1994).
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 X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RX PubMed=10331925; DOI=10.1006/jmbi.1999.2719;
RA Fritsche E., Paschos A., Beisel H.-G., Boeck A., Huber R.;
RT "Crystal structure of the hydrogenase maturating endopeptidase HYBD from
RT Escherichia coli.";
RL J. Mol. Biol. 288:989-998(1999).
CC -!- FUNCTION: Protease involved in the C-terminal processing of HybC, the
CC large subunit of hydrogenase 2. Specifically cleaves off a 15 amino
CC acid peptide from the C-terminus of the precursor of HybC.
CC -!- COFACTOR:
CC Name=Ni(2+); Xref=ChEBI:CHEBI:49786;
CC -!- SIMILARITY: Belongs to the peptidase A31 family. {ECO:0000305}.
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DR EMBL; U09177; AAA21592.1; -; Genomic_DNA.
DR EMBL; U28377; AAA69160.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76029.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77054.1; -; Genomic_DNA.
DR PIR; G65085; G65085.
DR RefSeq; NP_417467.1; NC_000913.3.
DR RefSeq; WP_001221939.1; NZ_SSZK01000023.1.
DR PDB; 1CFZ; X-ray; 2.20 A; A/B/C/D/E/F=1-159.
DR PDBsum; 1CFZ; -.
DR AlphaFoldDB; P37182; -.
DR SMR; P37182; -.
DR BioGRID; 4262374; 54.
DR BioGRID; 853231; 1.
DR DIP; DIP-9967N; -.
DR IntAct; P37182; 6.
DR STRING; 511145.b2993; -.
DR MEROPS; A31.001; -.
DR jPOST; P37182; -.
DR PaxDb; P37182; -.
DR PRIDE; P37182; -.
DR EnsemblBacteria; AAC76029; AAC76029; b2993.
DR EnsemblBacteria; BAE77054; BAE77054; BAE77054.
DR GeneID; 948982; -.
DR KEGG; ecj:JW2961; -.
DR KEGG; eco:b2993; -.
DR PATRIC; fig|1411691.4.peg.3736; -.
DR EchoBASE; EB1750; -.
DR eggNOG; COG0680; Bacteria.
DR HOGENOM; CLU_099037_0_0_6; -.
DR InParanoid; P37182; -.
DR OMA; RKMSSHQ; -.
DR PhylomeDB; P37182; -.
DR BioCyc; EcoCyc:EG11802-MON; -.
DR BioCyc; MetaCyc:EG11802-MON; -.
DR BRENDA; 3.4.23.B20; 2026.
DR EvolutionaryTrace; P37182; -.
DR PRO; PR:P37182; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0004190; F:aspartic-type endopeptidase activity; IEA:UniProtKB-KW.
DR GO; GO:0004175; F:endopeptidase activity; IDA:EcoCyc.
DR GO; GO:0008047; F:enzyme activator activity; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0036211; P:protein modification process; IBA:GO_Central.
DR GO; GO:0016485; P:protein processing; IDA:EcoCyc.
DR Gene3D; 3.40.50.1450; -; 1.
DR InterPro; IPR004419; Pept_A31_hyd_express.
DR InterPro; IPR023430; Pept_HybD-like_dom_sf.
DR InterPro; IPR000671; Peptidase_A31.
DR PANTHER; PTHR30302; PTHR30302; 1.
DR Pfam; PF01750; HycI; 1.
DR PRINTS; PR00446; HYDRGNUPTAKE.
DR SUPFAM; SSF53163; SSF53163; 1.
DR TIGRFAMs; TIGR00140; hupD; 1.
DR TIGRFAMs; TIGR00072; hydrog_prot; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Aspartyl protease; Hydrolase; Metal-binding; Nickel;
KW Protease; Reference proteome.
FT CHAIN 1..164
FT /note="Hydrogenase 2 maturation protease"
FT /id="PRO_0000201943"
FT BINDING 16
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 62
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT BINDING 93
FT /ligand="Ni(2+)"
FT /ligand_id="ChEBI:CHEBI:49786"
FT CONFLICT 160..164
FT /note="EAIHD -> SDS (in Ref. 1; AAA21592)"
FT /evidence="ECO:0000305"
FT STRAND 3..9
FT /evidence="ECO:0007829|PDB:1CFZ"
FT HELIX 14..17
FT /evidence="ECO:0007829|PDB:1CFZ"
FT HELIX 18..29
FT /evidence="ECO:0007829|PDB:1CFZ"
FT STRAND 36..42
FT /evidence="ECO:0007829|PDB:1CFZ"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:1CFZ"
FT HELIX 49..52
FT /evidence="ECO:0007829|PDB:1CFZ"
FT STRAND 56..63
FT /evidence="ECO:0007829|PDB:1CFZ"
FT STRAND 74..78
FT /evidence="ECO:0007829|PDB:1CFZ"
FT HELIX 81..86
FT /evidence="ECO:0007829|PDB:1CFZ"
FT HELIX 92..106
FT /evidence="ECO:0007829|PDB:1CFZ"
FT STRAND 112..119
FT /evidence="ECO:0007829|PDB:1CFZ"
FT STRAND 126..129
FT /evidence="ECO:0007829|PDB:1CFZ"
FT HELIX 132..135
FT /evidence="ECO:0007829|PDB:1CFZ"
FT HELIX 138..150
FT /evidence="ECO:0007829|PDB:1CFZ"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:1CFZ"
SQ SEQUENCE 164 AA; 17751 MW; F390F66529380FA8 CRC64;
MRILVLGVGN ILLTDEAIGV RIVEALEQRY ILPDYVEILD GGTAGMELLG DMANRDHLII
ADAIVSKKNA PGTMMILRDE EVPALFTNKI SPHQLGLADV LSALRFTGEF PKKLTLVGVI
PESLEPHIGL TPTVEAMIEP ALEQVLAALR ESGVEAIPRE AIHD
