Family N11

Family

Summary Holotypes Alignment Tree Genomes Literature

Summary for family N11

Family type peptidaseN11.001 - intein-containing chloroplast ATP-dependent peptide lyase (Chlamydomonas eugametos), MEROPS Accession MER0180157 (peptidase unit: 448-589, 729-904)
Content of familyFamily N11 includes self-cleaving proteins
History Identifier created: MEROPS 9.4 (31 January 2011)
An intein is a protein able to release itself from its precursor cleaving at both its N- and its C-terminus. The flanking regions are known as exteins, and release of the intein is accompanied by formation of a peptide bond between the two exteins. In the case of the Ceu clpP intein (N11.001) from Chlamydomonas moewusii, the intein is a DOD-type homing endonuclease, and the exteins, once spliced, become subunit clpP of the clp endopeptidase (S16.001).
Catalytic typeAsparagine
Active site residuesC448 N903 
Active siteThree residues are involved in activity, the first (Cys) and last (Asn or Gln) residues of the intein, and the first residue of the second portion of the extein (Cys, Ser or Thr). Each of these acts as a nucleophile in each of the three reactions that occur to excise the intein and splice the remaining portions of the extein. The thiol on the side chain of the first residue of the intein (Cys) attacks the carbonyl carbon of the preceding amino acid to generate a thiolester intermediate. Then transesterification occurs in which the first residue of the second portion of the extein (Cys, Ser or Thr) attacks the thioester. This results in a branched intermediate where the first portion of the extein is transfered to the side chain of the first residue of the second portion. The peptide bond between the first portion of the extein and the first residue of the intein is broken. The branched intermediate thus has two N-termini. Then the last residue of the intein, which is usually Asn, cyclizes to form a succinimide ring, which results in the breakage of the peptide bond between the Asn and the first residue of the second portion of the extein. The intein is thus released. The ester or thioester bond in the extein then rapidly undergoes an acyl rearrangement to form a normal peptide bond, which is thermodynamically more stable (Raghavan & Minnick, 2009). An example where the Asn is replaced by Gln is the hypothetical protein SRM_02212 from Salinibacter ruber. An example where Cys is the first residue of the second portion of the extein is the RfbB protein from Synechococcus, and an example where it is Thr is the Gp3 protein from mycobacterium phage LRRHood.
Activities and specificitiesThe only peptidase activity is cleavage at the start and end of the intein, which is then released. Once the intein is released, no further peptidase activity occurs.
Molecular structureNo structures have been solved for any member of the family, but because the catalytic residues are in the same order as in the other families of inteins, N9 and N10, N11 is included in clan PD and subclan PD(N), and the tertiary structures are assumed to be similar.
ClanPD
SubclanPD(N)
Distribution of family Bacteria details  
Archaea details  
Protozoa -  
Fungi details  
Plants details  
Animals -  
Viruses details  
Biological functions
Statistics for family N11Sequences:74
Identifiers:1
Identifiers with PDB entries:0
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
intein-containing chloroplast ATP-dependent peptide lyaseN11.001-
family N11 non-lyase homologuenon-peptidase homologue-
family N11 unassigned peptide lyaseunassigned-