Information on EC 3.4.23.B20 - HycD peptidase

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The expected taxonomic range for this enzyme is: Escherichia coli

EC NUMBER
COMMENTARY hide
3.4.23.B20
preliminary BRENDA-supplied EC number
RECOMMENDED NAME
GeneOntology No.
HycD peptidase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
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
show the reaction diagram
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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
?
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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 SUBSTRATES
NATURAL PRODUCTS
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
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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
P37182
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
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
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17000
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1 * 17000
17500
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calculated from nucleotide sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
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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
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli BL21 (DE3)