>TIGR01975 isoAsp_dipep beta-aspartyl peptidase; InterPro: IPR010229 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of proteins include metallopeptidases belonging to the MEROPS peptidase family M38 (clan MJ, beta-aspartyl dipeptidase family). This entry includes the beta-aspartyl dipeptidase from Escherichia coli, (3.4.19.5 from EC, IadA), which degrades isoaspartyl dipeptides and may unblock degradation of proteins that cannot be repaired. This entry also describes closely related proteins from other species (e.g. Clostridium perfringens, Thermoanaerobacter tengcongensis) that may have an equivalent in function. This family shows homology to dihydroorotases. The L-isoaspartyl derivative of Asp arises non-enzymatically over time as a form of protein damage. In this isomerisation, the connectivity of the polypeptide changes to pass through the beta-carboxyl of the side chain. Much but not all of this damage can be repaired by protein-L-isoaspartate (D-aspartate) O-methyltransferase..

Probab=99.90  E-value=2.3e-23  Score=168.61  Aligned_cols=138  Identities=17%  Similarity=0.128  Sum_probs=96.3

Q ss_pred             EEEECCEEECCCCCEEEEEEEEEECCEEEEECCCCCCCCCCCCCEEEEC-CCCEEECCEEECCCCCCCCCCCC---CCCH
Q ss_conf             6996429999888850001089979999983178655666788779988-79889517271411478999831---1437
Q gi|254780301|r    4 FVLNNTRIIDPSRDIDEVGAIIVENGIILAAGADALNAKFPTSALIHDC-TGLVAVPGIIDARVTLTGSPDEY---SKNI   79 (431)
Q Consensus         4 llI~n~~iid~~~~~~~~~~I~I~~gkI~~Ig~~~~~~~~~~~~~vID~-~G~~v~PGlID~H~Hl~~~~~~~---~~~~   79 (431)
T Consensus         2 ~llkg~~vY~Pe~--~GkkD~li~~~ki~~i~d~i~~~k~~~~~~vv~~~eG~i~vPGfID~HVHiiGGGGEgG~~TRTP   79 (391)
T TIGR01975         2 TLLKGLEVYAPEY--IGKKDILIVSDKIIAIADEIELTKDFVEVEVVEGLEGMIAVPGFIDQHVHIIGGGGEGGPKTRTP   79 (391)
T ss_pred             CCCCCCCCCCCCC--CCCCCEEEECCEEEEEECCCCCCCCCCCCEEEECCCCCEECCCCCCCCEEEEECCCCCCCCCCCH
T ss_conf             2011551358888--88421799788489860376566651253388157770873874147457840576886888843


Q ss_pred             HHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEECCCCCCCCCCCC
Q ss_conf             8899998707873212454556643331667777677664310122321000134432222222
Q gi|254780301|r   80 TTLSKEAVAGGITSIILMPLGMSSFLDEYTFIKYALEEIRVKSLINVYPTACLTSNMEGKEISE  143 (431)
Q Consensus        80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  143 (431)
T Consensus        80 E~~Ls~~t~~GvTtvVG~lGTDgi~R~m~~L~AKArAL~eEGvs~y~ltGaY~vP~~TlTgsv~  143 (391)
T TIGR01975        80 ELTLSDITKGGVTTVVGLLGTDGITRDMESLLAKARALEEEGVSCYVLTGAYEVPVRTLTGSVK  143 (391)
T ss_pred             HHECCCEEECCCEEEEEEEECCCCCCCCHHHHHHHHHHHHCCEEEEEEECCEECCCCCCCCCEE
T ss_conf             2230120112624898886278622584678999986520782699963331355200151124