Summary: Lysine-specific metallo-endopeptidase
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Lysine-specific metallo-endopeptidase Provide feedback
This is the catalytic region of aspzincins, a group of lysine-specific metallo-endopeptidases in the M35 family. They exhibit the following active-site architecture. The active site is composed of two helices and a loop region and includes the HExxH and GTxDxxYG motifs. In UniProt:P81054 His117, His121 and Asp130 coordinate to the catalytic zinc ligands. An electrostatically negative region composed of Asp154 and Glu157 attracts a positively charged Lys side chain of a substrate in a specific manner .
Nonaka T, Hashimoto Y, Takio K;, J Biochem. 1998;124:157-162.: Kinetic characterization of lysine-specific metalloendopeptidases from Grifola frondosa and Pleurotus ostreatus fruiting bodies. PUBMED:9644258 EPMC:9644258
Healy V, O'Connell J, McCarthy TV, Doonan S;, Biochem Biophys Res Commun. 1999;262:60-63.: The lysine-specific proteinase from Armillaria mellea is a member of a novel class of metalloendopeptidases located in Basidiomycetes. PUBMED:10448068 EPMC:10448068
Hori T, Kumasaka T, Yamamoto M, Nonaka N, Tanaka N, Hashimoto Y, Ueki U, Takio K;, Acta Crystallogr D Biol Crystallogr. 2001;57:361-368.: Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms. PUBMED:11223512 EPMC:11223512
McAuley KE, Jia-Xing Y, Dodson EJ, Lehmbeck J, Ostergaard PR, Wilson KS;, Acta Crystallogr D Biol Crystallogr. 2001;57:1571-1578.: A quick solution: ab initio structure determination of a 19 kDa metalloproteinase using ACORN. PUBMED:11679721 EPMC:11679721
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- the number of sequences which exhibit this architecture
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This example describes an architecture with one
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Clan MA is one of two zinc-dependent metallopeptidases that contain the HEXXH motif. The two histidines are zinc ligands. The structures of this clan show the active site is between its two sub-domains.
The clan contains the following 54 members:Aspzincin_M35 Astacin BSP DUF1570 DUF2201_N DUF2268 DUF3152 DUF3633 DUF3810 DUF4157 DUF45 DUF955 Enhancin HRXXH M60-like Peptidase_M1 Peptidase_M10 Peptidase_M11 Peptidase_M13 Peptidase_M2 Peptidase_M27 Peptidase_M3 Peptidase_M30 Peptidase_M32 Peptidase_M35 Peptidase_M36 Peptidase_M4 Peptidase_M41 Peptidase_M43 Peptidase_M48 Peptidase_M4_C Peptidase_M50 Peptidase_M50B Peptidase_M54 Peptidase_M56 Peptidase_M57 Peptidase_M6 Peptidase_M61 Peptidase_M64 Peptidase_M66 Peptidase_M7 Peptidase_M8 Peptidase_M9 Peptidase_M91 Peptidase_MA_2 Peptidase_U49 Reprolysin Reprolysin_2 Reprolysin_3 Reprolysin_4 Reprolysin_5 SprT-like WLM Zn_peptidase
We make a range of alignments for each Pfam-A family:
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Curation and family details
This family is new in this Pfam release.
|Seed source:||Pfam-B_2237 (release 26.0), pdb_1g12|
|Number in seed:||34|
|Number in full:||226|
|Average length of the domain:||142.80 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||48.57 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
|Download:||download the raw HMM for this family|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Aspzincin_M35 domain has been found. There are 9 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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