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Information on EC 3.4.23.B20 - HycD peptidase and Organism(s) Escherichia coli and UniProt Accession P37182

for references in articles please use BRENDA:EC3.4.23.B20
preliminary BRENDA-supplied EC number
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EC Tree
     3 Hydrolases
         3.4 Acting on peptide bonds (peptidases)
             3.4.23 Aspartic endopeptidases
                3.4.23.B20 HycD peptidase
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This record set is specific for:
Escherichia coli
UNIPROT: P37182
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Escherichia coli
Reaction Schemes
This enzyme specifically removes a 15-amino acid peptide from the C-terminus of the precursor of the large subunit of hydrogenase 2 [UniProt: P0ACE0] in Escherichia coli
Synonyms
endopeptidase of the hydrogenase 2 operon, HYBD, hydrogenase maturating endopeptidase HYBD, HypD, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
endopeptidase of the hydrogenase 2 operon
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hydrogenase maturating endopeptidase HYBD
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
precursor of the large subunit of hydrogenase 2 + H2O
?
show the reaction diagram
precursor of the large subunit of hydrogenase 2 + H2O
large subunit of hydrogenase 2 + propeptide of hydrogenase 2
show the reaction diagram
additional information
?
-
a construct in which the C-terminal extension from the large subunit of the hydrogenase 2 is fused to the mature part of the large subunit of hydrogenase 3 is neither processed by HybD nor by HycI (the endopeptidase specific for the large subunit of hydrogenase 3)
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
precursor of the large subunit of hydrogenase 2 + H2O
?
show the reaction diagram
the final step of maturation of [NiFe]-hydrogenases involves the activity of an endopeptidase which removes an oligopeptide from the C-terminus of the large subunit of hydrogenase 2 (UniProt: P0ACE0). The proteolytic maturation is followed by a conformational change, closing of the metal centre, its assembly with the small hydrogenase subunit and finally in the appearance of enzyme activity
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-
?
precursor of the large subunit of hydrogenase 2 + H2O
large subunit of hydrogenase 2 + propeptide of hydrogenase 2
show the reaction diagram
the maturation of [NiFe] hydrogenases includes formation of the nickel metallocenter, proteolytic processing of the metal center carrying large subunit, and its assembling with other hydrogenase subunits. The hydrogenase maturating enzyme HYBD specifically cleaves off a 15 amino acid peptide from the C terminus of the precursor of the large subunit of hydrogenase 2 (UniProt: P0ACE0)
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17000
1 * 17000
17500
calculated from nucleotide sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
1 * 17000
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of HYBD are grown at 20°C by vapor-diffusion using the hanging drop method. Crystal structure of HYBD at 2.2 A resolution. It consists of a twisted five-stranded beta-sheetsurrounded by four and three helices, respectively, on each side. A cadmium ion from the crystallization buffer binds to the proposed nickel-binding site and is penta-coordinated by Glu16, Asp62, His93, and a water molecule in a pseudo-tetragonal arrangement. HYBD is topologically related to members of the metzincins superfamily of zinc endoproteinases, sharing the central beta-sheet and three helices. In contrast to the metzincins, the metal-binding site of HYBD is localized at the C-terminal end of the beta-sheet
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified endopeptidases HycD is devoid of metal
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli BL21 (DE3)
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Theodoratou, E.; Paschos, A.; Mintz-Weber, S.; Bock, A.
Analysis of the cleavage site specificity of the endopeptidase involved in the maturation of the large subunit of hydrogenase 3 from Escherichia coli
Arch. Microbiol.
173
110-116
2000
Escherichia coli (P37182)
Manually annotated by BRENDA team
Theodoratou, E.; Paschos, A.; Magalon, A.; Fritsche, E.; Huber, R.; Bock, A.
Nickel serves as a substrate recognition motif for the endopeptidase involved in hydrogenase maturation
Eur. J. Biochem.
267
1995-1999
2000
Escherichia coli (P37182)
Manually annotated by BRENDA team
Menon, N.K.; Chatelus, C.Y.; Dervartanian, M.; Wendt, J.C.; Shanmugam, K.T.; Peck, H.D., Jr.; Przybyla, A.E.
Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2
J. Bacteriol.
176
4416-4423
1994
Escherichia coli (P37182)
Manually annotated by BRENDA team
Theodoratou, E.; Huber, R.; Bck A.
[NiFe]-Hydrogenase maturation endopeptidase: structure and function
Biochem. Soc. Trans.
33
108-111
2005
Escherichia coli (P37182)
Manually annotated by BRENDA team
Fritsche, E.; Paschos, A.; Beisel, H.G.; Bock, A.; Huber, R.
Crystal structure of the hydrogenase maturating endopeptidase HYBD from Escherichia coli
J. Mol. Biol.
288
989-998
1999
Escherichia coli (P37182), Escherichia coli
Manually annotated by BRENDA team