>pfam03734 YkuD L,D-transpeptidase catalytic domain. This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.

Probab=99.55 E-value=1.2e-14 Score=110.08 Aligned_cols=111 Identities=30% Similarity=0.402 Sum_probs=83.6 Q ss_pred HHHHHHCCCEEE-EEEECCEEEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCHHHHHHCCEE Q ss_conf 345420452489-9998885555412313887777855421003898448778876677777777764186778749939 Q gi|254780350|r 194 RYVLVNIPAASL-EAVENGKVGLRSTVIVGRVDRQTPILHSRINRIMFNPYWVIPRSIIQKDMMALLRQDPQYLKDNNIH 272 (431) Q Consensus 194 ~~v~VNip~~~l-~~~e~g~~~~~~~viVGk~~~~TP~~~~~i~~iv~NP~W~vP~sI~~~eilpk~~~dp~yl~~~~~~ 272 (431) T Consensus 2 ~~I~Vd~~~~~l~~~~~~g~~v~~~~vs~G~~~~~TP~G~~~i~~k~~~~~~~~~~~~~~-------------------- 61 (122) T pfam03734 2 RVIVVDLSEQRLLLLYENGKLVLTYPVSVGRGDTPTPLGTFTITEKVENPTWAPGPGNGL-------------------- 61 (122) T ss_pred CEEEEECCCCEEEEEEECCEEEEEEEEEECCCCCCCCCCEEEEEEEEECCCCCCCCCCCC-------------------- T ss_conf 299998943899999759999999778858899988665699899875884578675554-------------------- Q ss_pred EECCCCCEECCCCCCCCCCCCCCCCEEECCCCCCCCEEEEEECCCCCEEEECCCCCHHHCCCCCCCCCCCCEECCC--HH Q ss_conf 9938997835020470104457722472689998631489531588766813889832328655554115034479--89 Q gi|254780350|r 273 MIDEKGKEVFVEEVDWNSPEPPNFIFRQDPGKINAMASTKIEFYSRNNTYMHDTPEPILFNNVVRFETSGCVRVRN--II 350 (431) Q Consensus 273 i~~~~g~~vdp~~i~w~~~~~~~~~~rQ~PGp~NaLG~vkf~f~N~~~iyLHdTP~~~lF~~~~Ra~ShGCVRv~n--p~ 350 (431) T Consensus 62 --------------------------------~~~~~~~~~~~~~~~~i~iH~~~~~~~~~~g-~~~ShGCIrl~~~d~~ 108 (122) T pfam03734 62 --------------------------------GYVKFLDPWAFPNGGGIYIHGTGTPDLFSGG-APRSHGCIRLSNEDAK 108 (122) T ss_pred --------------------------------CCCCCCCEEEECCCCCEEEECCCCCCCCCCC-CCCCCCCCCCCHHHHH T ss_conf --------------------------------6876552468727984389668888422479-8467760157999999 Q ss_pred HHHHHHH Q ss_conf 9999984 Q gi|254780350|r 351 DLDVWLL 357 (431) Q Consensus 351 ~La~~ll 357 (431) T Consensus 109 ~l~~~v~ 115 (122) T pfam03734 109 ELYDWVL 115 (122) T ss_pred HHHHCCC T ss_conf 9997099

HHsearch alignment for GI: 254780350 and conserved domain: pfam03734