1ZAT,3TUR,4Z7A,4XXT,2HKL,4LZH,4Y4V,3ZQD,4A1I,1Y7M,4A1K,4XZZ,3TX4,5DU7,5D7H,4QR7,4GSQ,3VYO,5K69,5E51,4XVO,4JMN,4K73,3VYN,3VYP,4HUC,4QTF,5DCC,5DVP,3U1P,5BMQ,4LPQ,3ZG4


Conserved Protein Domain Family
YkuD_like

?
cd16913: YkuD_like 
Click on image for an interactive view with Cn3D
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD
Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.
Statistics
?
PSSM-Id: 341130
Aligned: 695 rows
Threshold Bit Score: 31.1253
Created: 13-Jul-2015
Updated: 2-Oct-2020
Structure
?
Program:
Drawing:
Aligned Rows:
 
polypeptideputative active
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:polypeptide substrate binding site [polypeptide binding site]
Evidence:
  • Structure:3TUR; Mycobacterium tuberculosis L,D-Transpeptidase 2 with bound peptidoglycan fragment, contacts 4A

Sequence Alignment
?
Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
1ZAT_A       128 YIEVDLe------nQHMWYYkdg--kvALETDIVSGkpt-----------------tpTPAGVFYVwNKEEDatlkgtnd 182 Enterococcus fa...
3TUR_A       133 IATADDn------tKILTVRvng--evVKSMPTSMGkds-----------------tpTANGIYIVgSRYKHiimdssty 187 Mycobacterium t...
Q28VD0        13 ICTSLKacssgmspEDLVLTpsglrfwGARLPFTVGrggvvrd--------kregdggTPVGTHRIvGCLYRadrgpkpc 84  Jannaschia sp. ...
Q89WQ7        29 AIRVKPaag---npRRGWLTa-----gALTIPVALGrggilan--------kregdggTPRGSFRPrRLWWRgdrhsrpq 92  Bradyrhizobium ...
WP_039722480   4 TVTVHRapg---hrQRGLLVg-----gPRVLPCALGrggpgvlkreg-dgvtpaggplRPLWGYWRaDRGPRpttalrmi 74  Lyngbya conferv...
WP_012091152  12 IIDVRAkpg---hkTRGLLVa-----gNLVLECALGkggisaf--------kregdgaTPLATMRLlYGYRRgdkgmlps 75  Ochrobactrum an...
WP_015822172  26 LLRVRPlpg---dpTRGTLIa-----gGVVIPCALGrsgittq--------kregdgaSPRGIFRLrGGFYRpdrfpvrp 89  Methylobacteriu...
EAP77072       5 DVISENmtdytvspDDMVLTarglrfqGRLYPCTIGrgglsrt--------kregdgaTPVGIHHVvGMFYRadrmprpa 76  Roseovarius nub...
WP_043759476  15 DIRVRAtvg---drRRGQLLv-----gPAVIPCALGaggivid--------kregdggSPRGRFRLrAGAYRpdhlgirp 78  Streptomyces pu...
ABI78093      55 VVIVDYsrh--sreERLYVVnle-tgtVTAYRAAHGlgsdpdhdgyldsfssvpesqaSPQGAFRIaEAYHGk------- 124 Hyphomonas nept...
Feature 1                                                                           ##  #        
1ZAT_A       183 d--------------------------------------gtpyespvNYWMPIDw-----------tGVGIHDSdwqpey 213 Enterococcus fa...
3TUR_A       188 gvp---------------------------------vnspngyrtdvDWATQISy-----------sGVFVHSApwsvga 223 Mycobacterium t...
Q28VD0        85 dwavpigpndlwsddeas----ddynlmvrrpymgtaerlargdplyDIVLITDwnwpea-qpgrgsAIFIHQWrgp--- 156 Jannaschia sp. ...
Q89WQ7        93 tflpariitgedawcedph--drhynqgirlgegqggdrlkradhlyDFIIEIDhntrpr-iagrgsAVFLHLArdn--- 166 Bradyrhizobium ...
WP_039722480  75 ptragdgwcdapthpa--------ynrpvrlpfaashetmwrtdalyDICIVLDwnmepgrardrgsAIFAHLAkdg--- 143 Lyngbya conferv...
WP_012091152  76 srlplgrirrldgwcdass--danynrpvrlpyaashedmwrrddlyDVCIVMDwniapr-rrgcgsAIFFHLArpg--- 149 Ochrobactrum an...
WP_015822172  90 vsalplratrrddgwcdapqdrrynrpirlpstaasaeqlwrddglyDLVIDLDynrgpi-rpgrgsAIFLHIArsg--- 165 Methylobacteriu...
EAP77072      77 hwaeptglrdlwsddsrap--eynqlvrapyaashetmrradplydlVMITDWNypeae---pergsCIFIHRWrrk--- 148 Roseovarius nub...
WP_043759476  79 rtllplratrpddgwcdesrdrrynrpirlpapgisaesmwrgdglyDVVIDLDynrapi-rkgrgsAIFLHIArdg--- 154 Streptomyces pu...
ABI78093     125 ----------------------------------------------hGRSVRLDglddtn-qtarsrAIVIHAAsyaepd 157 Hyphomonas nept...
Feature 1                  #### #                      
1ZAT_A       214 gg-dlwktrgSHGCINTppSVMKELFGMVekGTPVLVF 250 Enterococcus faecium
3TUR_A       224 ----qghtntSHGCLNVspSNAQWFYDHVkrGDIVEVV 257 Mycobacterium tuberculosis
Q28VD0       157 -------grsTEGCVAVsrRHLRWIVPRInhGTRLIVP 187 Jannaschia sp. CCS1
Q89WQ7       167 -------fgpTAGCVSMtkSAILQLLRRLgpRTRIIIG 197 Bradyrhizobium japonicum
WP_039722480 144 -------yppTEGCIALarRDMVWLLARIdrRTQMSVS 174 Lyngbya confervoides
WP_012091152 150 -------ytpTEGCIALrrADMARLLPHLtdRTVIRVL 180 Ochrobactrum anthropi
WP_015822172 166 -------yrpTEGCVALkpADLLRLLRRLgpGTRMKIG 196 Methylobacterium extorquens
EAP77072     149 -------gfpTAGCLGLrpDHLLQIAGRIepGARFVVP 179 Roseovarius nubinhibens ISM
WP_043759476 155 -------yrpTEGCVALarADLLRLLRRLgpRTHLRIG 185 Streptomyces purpurogeneiscleroticus
ABI78093     158 hlarygklgrSNGCIVFseADLATFLEDVpeGTFLFIG 195 Hyphomonas neptunium ATCC 15444

| Disclaimer | Privacy statement | Accessibility |
NCBI Home NCBI Search NCBI SiteMap