>TIGR00666 PBP4 D-alanyl-D-alanine carboxypeptidase/D-alanyl-D-alanine-endopeptidase; InterPro: IPR000667 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . 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 family of serine peptidases belong to MEROPS peptidase family S13 (D-Ala-D-Ala carboxypeptidase C, clan SE). The predicted active site residues for members of this family and family S12 occur in the motif SXXK. D-Ala-D-Ala carboxypeptidase C is involved in the metabolism of cell components ; it is synthesised with a leader peptide to target it to the cell membrane . After cleavage of the leader peptide, the enzyme is retained in the membrane by a C-terminal anchor . There are three families of serine-type D-Ala-D-Ala peptidase (designated S11, S12 and S13), which are also known as low molecular weight penicillin-binding proteins . Family S13 comprises D-Ala-D-Ala peptidases that have sufficient sequence similarity around their active sites to assume a distant evolutionary relationship to other clan members; members of the S13 family also bind penicillin and have D-amino-peptidase activity. Proteases of family S11 have exclusive D-Ala-D-Ala peptidase activity, while some members of S12 are C beta-lactamases . ; GO: 0004185 serine carboxypeptidase activity, 0006508 proteolysis.

Probab=96.23  E-value=0.0031  Score=38.23  Aligned_cols=176  Identities=14%  Similarity=0.166  Sum_probs=117.0

Q ss_pred             HHHHHHHCCCCCCCCCCC-CCHHHHCCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHC-------CHHHHHH
Q ss_conf             999975558988554111-53676124544322578856883024578899877777654554201-------0057899
Q gi|254780698|r   88 IIFEYLQSKKLHLNTQIP-VSKTAATQNPSKLYLKEKTYFTTEQGILALITRSANDVSTAFGEFIS-------GSEKKFA  159 (336)
Q Consensus        88 v~le~i~~g~i~~~~~v~-is~~a~~~~~s~~~l~~g~~~tv~dLl~~lli~S~NdAa~alAe~i~-------Gs~~~Fv  159 (336)
T Consensus       233 ~~~~~Lk~~GI~~~g~~~r~~~---~~~~~~~PLa~~~S~PL~~Ll~~mmk~SdN~~Ae~l~r~~~~~~~~~~~Sw~~g~  309 (427)
T TIGR00666       233 ILKQKLKQLGITVSGKILRAAQ---APEAGQVPLASHQSAPLIDLLKKMMKKSDNLIAEALFREVAVARIKRPGSWQKGV  309 (427)
T ss_pred             HHHHHHHHCCCCEEEEEEECCC---CCCCCCCCHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHH
T ss_conf             9999999718962136774378---8875656533214886689999986210633378887631543126752078889


Q ss_pred             HHHHHHHHHHCC--CCCCEECCCCCCCCCCCCCHHHHHHHHHHHC-CCCEEEEEEEEEEEEEECCEEE-EEE--CHHCCC
Q ss_conf             988876887266--1222002454333344530134555554201-3620467761156543478699-721--010257
Q gi|254780698|r  160 ILMSNKAKKIGM--QNTIYKNASGLHDKNQITTARDQAILGILLR-KNFPQYYKYFSIRKFRYRNRII-TNH--NKLLNK  233 (336)
Q Consensus       160 ~~MN~~A~~lGl--~~t~f~np~Gl~~~~~~tta~Dla~l~~~~~-~~~p~~~~~~s~~~~~~~~~~~-~n~--N~lL~~  233 (336)
T Consensus       310 ~av~s~L~~~G~d~~~~~L~DGSGLSr~n-lv~p~tl~q~L~~~aGP~~~~~~~~~~~LP~AG~~Gtlv~~Rl~~~~~~~  388 (427)
T TIGR00666       310 EAVKSILQEAGVDTGNVILRDGSGLSRHN-LVTPKTLVQLLQYIAGPDQSAKLAYLDSLPVAGRSGTLVGERLLDGLKDT  388 (427)
T ss_pred             HHHHHHHHHCCCEECCEEEEECCCCCHHH-HHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             99987544404000352787145525445-66499999999985388871135688734446899840478888766177


Q ss_pred             -CCCCEEEEECCCCCCCCEEEEEEE-ECCEEEEEEEE
Q ss_conf             -687005652242333717999999-78979999981
Q gi|254780698|r  234 -MHNIDGIKTGYTRNSGFNIVTSLR-YKDDPIVAVVM  268 (336)
Q Consensus       234 -~~g~~G~KTG~T~~AG~clv~~a~-~~g~~lI~Vvl  268 (336)
T Consensus       389 p~~GkvrAKTGS-L~gV~sL~G~~t~~~G~~~aF~~~  424 (427)
T TIGR00666       389 PLVGKVRAKTGS-LTGVYSLAGYVTNASGKKLAFSFL  424 (427)
T ss_pred             CCCCEEEEECCC-CCEEEEEEEEEECCCCCEEEEEEE
T ss_conf             987437752233-421323477788368988999888