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Protein

Hydrogenase 2 maturation protease

Gene

hybD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Protease involved in the C-terminal processing of HybC, the large subunit of hydrogenase 2. Specifically cleaves off a 15 amino acid peptide from the C-terminus of the precursor of HybC.

Cofactori

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi16 – 161Nickel
Metal bindingi62 – 621Nickel
Metal bindingi93 – 931Nickel

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Aspartyl protease, Hydrolase, Protease

Keywords - Ligandi

Metal-binding, Nickel

Enzyme and pathway databases

BioCyciEcoCyc:EG11802-MONOMER.
ECOL316407:JW2961-MONOMER.
BRENDAi3.4.23.B20. 2026.

Protein family/group databases

MEROPSiA31.001.

Names & Taxonomyi

Protein namesi
Recommended name:
Hydrogenase 2 maturation protease (EC:3.4.23.-)
Gene namesi
Name:hybD
Ordered Locus Names:b2993, JW2961
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11802. hybD.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 164164Hydrogenase 2 maturation proteasePRO_0000201943Add
BLAST

Proteomic databases

PaxDbiP37182.
PRIDEiP37182.

Interactioni

Protein-protein interaction databases

BioGridi4262374. 10 interactions.
DIPiDIP-9967N.
IntActiP37182. 6 interactions.
STRINGi511145.b2993.

Structurei

Secondary structure

1
164
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 97Combined sources
Helixi14 – 174Combined sources
Helixi18 – 2912Combined sources
Beta strandi36 – 427Combined sources
Helixi46 – 483Combined sources
Helixi49 – 524Combined sources
Beta strandi56 – 638Combined sources
Beta strandi74 – 785Combined sources
Helixi81 – 866Combined sources
Helixi92 – 10615Combined sources
Beta strandi112 – 1198Combined sources
Beta strandi126 – 1294Combined sources
Helixi132 – 1354Combined sources
Helixi138 – 15013Combined sources
Turni151 – 1533Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CFZX-ray2.20A/B/C/D/E/F1-159[»]
ProteinModelPortaliP37182.
SMRiP37182. Positions 1-159.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP37182.

Family & Domainsi

Sequence similaritiesi

Belongs to the peptidase A31 family.Curated

Phylogenomic databases

eggNOGiENOG4108USZ. Bacteria.
COG0680. LUCA.
HOGENOMiHOG000278719.
InParanoidiP37182.
KOiK03605.
OMAiDHLIVAD.
OrthoDBiEOG6W9X9G.
PhylomeDBiP37182.

Family and domain databases

Gene3Di3.40.50.1450. 1 hit.
InterProiIPR004419. Pept_A31_hyd_express.
IPR023430. Pept_HybD-like_dom.
IPR000671. Peptidase_A31.
[Graphical view]
PfamiPF01750. HycI. 1 hit.
[Graphical view]
PRINTSiPR00446. HYDRGNUPTAKE.
SUPFAMiSSF53163. SSF53163. 1 hit.
TIGRFAMsiTIGR00140. hupD. 1 hit.
TIGR00072. hydrog_prot. 1 hit.

Sequencei

Sequence statusi: Complete.

P37182-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MRILVLGVGN ILLTDEAIGV RIVEALEQRY ILPDYVEILD GGTAGMELLG
60 70 80 90 100
DMANRDHLII ADAIVSKKNA PGTMMILRDE EVPALFTNKI SPHQLGLADV
110 120 130 140 150
LSALRFTGEF PKKLTLVGVI PESLEPHIGL TPTVEAMIEP ALEQVLAALR
160
ESGVEAIPRE AIHD
Length:164
Mass (Da):17,751
Last modified:October 1, 1996 - v2
Checksum:iF390F66529380FA8
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti160 – 1645EAIHD → SDS in AAA21592 (PubMed:8021226).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09177 Genomic DNA. Translation: AAA21592.1.
U28377 Genomic DNA. Translation: AAA69160.1.
U00096 Genomic DNA. Translation: AAC76029.1.
AP009048 Genomic DNA. Translation: BAE77054.1.
PIRiG65085.
RefSeqiNP_417467.1. NC_000913.3.
WP_001221939.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76029; AAC76029; b2993.
BAE77054; BAE77054; BAE77054.
GeneIDi948982.
KEGGiecj:JW2961.
eco:b2993.
PATRICi32121402. VBIEscCol129921_3088.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09177 Genomic DNA. Translation: AAA21592.1.
U28377 Genomic DNA. Translation: AAA69160.1.
U00096 Genomic DNA. Translation: AAC76029.1.
AP009048 Genomic DNA. Translation: BAE77054.1.
PIRiG65085.
RefSeqiNP_417467.1. NC_000913.3.
WP_001221939.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1CFZX-ray2.20A/B/C/D/E/F1-159[»]
ProteinModelPortaliP37182.
SMRiP37182. Positions 1-159.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262374. 10 interactions.
DIPiDIP-9967N.
IntActiP37182. 6 interactions.
STRINGi511145.b2993.

Protein family/group databases

MEROPSiA31.001.

Proteomic databases

PaxDbiP37182.
PRIDEiP37182.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76029; AAC76029; b2993.
BAE77054; BAE77054; BAE77054.
GeneIDi948982.
KEGGiecj:JW2961.
eco:b2993.
PATRICi32121402. VBIEscCol129921_3088.

Organism-specific databases

EchoBASEiEB1750.
EcoGeneiEG11802. hybD.

Phylogenomic databases

eggNOGiENOG4108USZ. Bacteria.
COG0680. LUCA.
HOGENOMiHOG000278719.
InParanoidiP37182.
KOiK03605.
OMAiDHLIVAD.
OrthoDBiEOG6W9X9G.
PhylomeDBiP37182.

Enzyme and pathway databases

BioCyciEcoCyc:EG11802-MONOMER.
ECOL316407:JW2961-MONOMER.
BRENDAi3.4.23.B20. 2026.

Miscellaneous databases

EvolutionaryTraceiP37182.
PROiP37182.

Family and domain databases

Gene3Di3.40.50.1450. 1 hit.
InterProiIPR004419. Pept_A31_hyd_express.
IPR023430. Pept_HybD-like_dom.
IPR000671. Peptidase_A31.
[Graphical view]
PfamiPF01750. HycI. 1 hit.
[Graphical view]
PRINTSiPR00446. HYDRGNUPTAKE.
SUPFAMiSSF53163. SSF53163. 1 hit.
TIGRFAMsiTIGR00140. hupD. 1 hit.
TIGR00072. hydrog_prot. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2."
    Menon N.K., Chatelus C.Y., Dervartanian M., Wendt J.C., Shanmugam K.T., Peck H.D. Jr., Przybyla A.E.
    J. Bacteriol. 176:4416-4423(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / TG1.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli."
    Fritsche E., Paschos A., Beisel H.-G., Boeck A., Huber R.
    J. Mol. Biol. 288:989-998(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).

Entry informationi

Entry nameiHYBD_ECOLI
AccessioniPrimary (citable) accession number: P37182
Secondary accession number(s): Q2M9K2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1996
Last modified: January 20, 2016
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Peptidase families
    Classification of peptidase families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.