2HKL,5E51,4XZZ


Conserved Protein Domain Family
YkuD

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pfam03734: YkuD 
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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.
Statistics
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PSSM-Id: 397687
Aligned: 168 rows
Threshold Bit Score: 32.7077
Threshold Setting Gi: 134266471
Created: 20-May-2020
Updated: 7-Aug-2020
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
2HKL_C        126 DTYIEVDLENqHM-WYYKDGKVALETDIVSGKpTTPTPAGVFYVwnkeedatlkgtnddgt------------------- 185 Enterococcus f...
Q7X2V6         87 DIRLTLNVPT-FRlTLWQNGKEVKSYYIGVGMkEHPLDIGAREAreiiwnpawipppsdwvremkgvs------------ 153 uncultured Aci...
EAV45104      418 ERKVFINQAA-FTaTYTAPGEDPLSMRVVVGkkSNQTNFFYDKIqiveynpywgvpysiivnemlpklakdpsyldragy 496 Labrenzia aggr...
OXE97688      324 DEYVMVNIPS-FRlIYVKDGKYDLVSDVFVGtrMTETVIFSGNIdrivfspywyvpasiiknelklkmaedknylad--- 399 Flavobacterium...
jgi:Plav_2903 164 DRYVFVNIAG-QEvEAVNNGIVEFREPVIVGkqDRQTPEITSEVnsitfnpywyvpksiamadmlpkiranpdylqrqgi 242 Parvibaculum l...
WP_012253006  182 RRFVITNIPA-ALvQTVENGQVVTLHAAGVGkiDRQSPIMNTKAtqinfnptwtvpasivrkdlipkmqkdpnyltdnki 260 Methylorubrum ...
Q89RI8        201 QRYVVVNIPA-AFaEAVENDVVVRRYRVIVGktEKPSPTLTAQItsvvlnptwtvpssiakteisahmrkdptylsrmhm 279 Bradyrhizobium...
jgi:Ssed_2377 257 EKLVWINIPG-YQlSIFEQGSVTLQMKVIIGkpSSPTPILSTYLtkltinpswrppasiiksellplnaaepgylnhkqf 335 Shewanella sed...
Q0HU27        314 ANYLIVNLAG-YElLLFKDNSLSWRTDIIIGkiNAKTPLFKSKLkyvvvnptwtvprsisteiinhlrkdpdylqkkhfk 392 Shewanella sp....
jgi:Swit_0490 356 TRHVVVDAAS-ARlWYYEGGKQRAMMRVVVGapETETPMLAGMVryavlnpywnvpdyliqrrlapkivagatpaslrme 434 Sphingomonas w...
2HKL_C        186 --------------------------------------pyespvnywmpidwtgVGIHDSDWQPEyggdlwktRG--SHG 225 Enterococcus f...
Q7X2V6        154 ------------------------------pgevikasdprnplgklkiplgdsYLIHQARGWSd-------vGNlvSHG 196 uncultured Aci...
EAV45104      497 evttpggr---qisssavdwyavaskqqsvnvrqypgssnalgevkilfpnkhhIYMHDTPAKSLfk----kdMRaySHG 569 Labrenzia aggr...
OXE97688      400 ----------------------hnmewnggsvrqkpgpnnslglvkfmfpnpndIYLHDTPAKSLfd----feKRtfSHG 453 Flavobacterium...
jgi:Plav_2903 243 rvlqgwdtn-irelnprnidwsnprineayyfrqdpgpgnslgslkinfpnnqaIFLHDTPTKTLfg----rqERnfSSG 317 Parvibaculum l...
WP_012253006  261 rilsggq-----eisprsvnwnsdegtrytyrqdsgadfnsmgvvrinipnahgVFMHDTNSRGVfg----ddFRfiSSG 331 Methylorubrum ...
Q89RI8        280 evldahd-----npidphsvdwsgthtpnftvrqqngtfnalgavkidmpnaysVYMHDTNQRNLfs----ddYRfdSHG 350 Bradyrhizobium...
jgi:Ssed_2377 336 elhgvglnkkhviklgdvdskqlptllrqyrlvqapgednalgkmrftivnrhsIYLHDTPAKQLfk----rnVRalSHG 411 Shewanella sed...
Q0HU27        393 vvegsgt----pvdasgidwhsmtrknfpywfvqepgednslgvvkfifpnqysIYLHDTPAKSLfe----qtDRafSHG 464 Shewanella sp....
jgi:Swit_0490 435 vlsdwsasp-rrlagdevdwpavaagrklvrmrqlpgrdnamgrvkfifpndlgIYLHDTPDKGLls----kaDRhlSNG 509 Sphingomonas w...
2HKL_C        226 SINTppSVMKELFGMVE-----------------------KG-T-----------------------------PVLV 249 Enterococcus faecium
Q7X2V6        197 CVRMprPELYDLADK------------------------------------------------------------IV 213 uncultured Acidob...
EAV45104      570 CIRL--QDPKAMAAAVLgkskdyvss-----risggqneqERvTgd--------------------------iPVYV 613 Labrenzia aggrega...
OXE97688      454 CINV--RDAKKLALEILkdnpdwpvdki-ndamsgekettCMlKnk--------------------------iPIYI 501 Flavobacterium jo...
jgi:Plav_2903 318 CVRV--QNVRGLVSWLMqgdssewdaarvarsvdsrqyrnVSlAt----------------------------PVPI 364 Parvibaculum lava...
WP_012253006  332 CVRV--QNVREYITWLLkdtp-------------------------------------------------gwdRTRV 357 Methylorubrum ext...
Q89RI8        351 CSRV--DNVRDLAAWLLkdqp-------------------------------------------------kwsRAAI 376 Bradyrhizobium ja...
jgi:Ssed_2377 412 CIRL--EKPIALSSYLVetderarelq---kavggsgtrhFSlSsp--------------------------iPVYI 457 Shewanella sedimi...
Q0HU27        465 CIRV--KDPLVLADKLLsananwssntl-ssklsegktenLFlDepldilimywtvtlkdgkikfyndvykrdPVLI 538 Shewanella sp. MR-7
jgi:Swit_0490 510 CIRL--QDAPGLYRLMFgrplpaaskq-------------------------------------perdvalpaPIPV 547 Sphingomonas witt...
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