Conserved Protein Domain Family
PLPDE_III_DSD_D-TA_like_3

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cd06814: PLPDE_III_DSD_D-TA_like_3 
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes Similar to D-Serine Dehydratase and D-Threonine Aldolase, Unknown Group 3
This subfamily is composed of uncharacterized bacterial proteins with similarity to eukaryotic D-serine dehydratases (DSD) and D-threonine aldolases (D-TA). DSD catalyzes the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. D-TA reversibly catalyzes the aldol cleavage of D-threonine into glycine and acetaldehyde, and the synthesis of D-threonine from glycine and acetaldehyde. DSD and D-TA are fold type III PLP-dependent enzymes, similar to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on their similarity to AR, it is possible members of this family also form dimers in solution.
Statistics
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PSSM-Id: 143489
View PSSM: cd06814
Aligned: 11 rows
Threshold Bit Score: 519.586
Threshold Setting Gi: 126738650
Created: 18-Jun-2008
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
Feature 1:active site [active site]
Evidence:
  • Comment:Based on the binding of the PLP cofactor and substrate analogs to other members of the superfamily.
  • Comment:The active site is composed of residues from both subunits of the dimer. There are two active sites in the functional dimer.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                               # #                    #                 
YP_957387     49 ALSEAGLATPTLVLDQGGLDYNLSALNSHLn-GEYHYRIVVKSLPSLPLLQRIMAaTGSNRLMVFHQPFLNTVAEALPqa 127 Marinobacter aq...
ZP_01075537   47 ALDKAQQSKPSLVIDKSLLLENIKVLKQHIs-GRFDYRIVAKSLPSIPLLKLIMEtANTQKLMVFHQPFLNQVATELPhs 125 Marinomonas sp....
YP_001189415  39 LLQQEGNGIPALLLDLDRLDANADLLAERLn-GRLGLRLVSKSLASVGLLEYLAKrLQTQRFMVFHQPQLNRLARSFPqa 117 Pseudomonas men...
EAZ61229      20 ELKANGPMCPVLLIDLDRLDHNIDVVMRSVrrGGKHLRLVEKSLPSPGLLAYIARrAGTRRLMSFHQPFLNHDAVAFAda 99  Pseudomonas aer...
NP_900711     21 ALRQAGIAEPTLVLDRQRLRANIRRISDHLa-GKMALRVVVKSLPCPALLAEAALlAGSRRQMLFSLPQLEAMAKGER-- 97  Chromobacterium...
YP_164851     12 ALIAAGRQLPTLVVDTERLAANMAAVRRMTa-PSLALRVVEKSLPAPDLLRVVIAgLETNRLMSFHLPFVQQAAAAFPea 90  Silicibacter po...
NP_108350     11 ALKTAGIFQPCLLLDRDRVDGNIALVKARLd-PSLAVRLVDKSLACLPLLSHIGKkVGTDRFMTFHPPISAAVLKAFRda 89  Mesorhizobium l...
ZP_01754355   18 MLRQTGVTGPCLILDKGRLMHNLALARERLh-PGVEVRVVAKSLAAPPLLDLAMEqLDARGVMSFSAPMLEELLHLRPna 96  Roseobacter sp....
ZP_01615990   43 LLKEKGPGRPVMMIDVDRMNHNIDQISNSVg-PEKTYRIVVKSLPSMDLLKHIMKrANTNALMVFHQPFLNAIVDAFPea 121 marine gamma pr...
ZP_01307187   44 ALKEQSIGTPRMLVDYDQLLQNVKTLTGHIk-PRFDYRIVAKSLPSIELLQVVMKaADTNRLMLFHQPFLSQVAKRLPda 122 Oceanobacter sp...
EDY86751      37 VYQSNGLSEPRLIIDGQRLDQNIDSLVQKI--GSDRYRIVAKSLPSLPLLRHVMArANTRKLMVFHRPFLSVIVREIPda 114 gamma proteobac...
Feature 1            #                                                             #      #      
YP_957387    128 DVLMGKPLPVAAVDRFYRQltsst-----sgfrPEQQLQWLVDSRQRLEAYEGFARSQQrrLRINLEIDIGLHRGGFTDt 202 Marinobacter aq...
ZP_01075537  126 DVLLGKPLPVNAAAKFYQVferqpkkntqeqfqPERQLQWLIDSPHRLNQYQNLAHSLKinMLINIELDIGFHRGGVADd 205 Marinomonas sp....
YP_001189415 118 DLLLGKPMPVHAALNFYRQlpgh------igftPARQLTWLIDSAERLRQYAELARALGqpLRIALEIDIGMARGGFRDp 191 Pseudomonas men...
EAZ61229     100 DILLGKPLPVRSAELFYREhkg--------afdPARQLQWLIDTPQRLRQYLALAQGLGtrMRVNIELDVGLHRGGVADq 171 Pseudomonas aer...
NP_900711     98 DILLGKPLPAAAALAFYRQfsda-------afrPERQLQWLVDTPERLAQYRELARGQHlhLRLNFEIDVGLHRGGVADi 170 Chromobacterium...
YP_164851     91 DILLGKPMPVGAVAGTSPT--------------LDAQVHWLIDSPERLAEYAALAAQSDraLRICLEVDIGLHRGGFSLa 156 Silicibacter po...
NP_108350     90 DLLYGKPMPVGAARAALVKgd-----------aDWSRVCWLIDTQERLAEYGALADEIGteLRIAFEIDVGLHRGGFASp 158 Mesorhizobium l...
ZP_01754355   97 EHLLGKPLPAPAAARILDRnv-----------rARDQVIWLIDTLERAQQYDALARERGlvLPIAVELDVGLHRGGFTTk 165 Roseobacter sp....
ZP_01615990  122 DILMGKPMPITAVATFYNTltrs-------aaaASQQIQWLIDTPERLIQYQQLANKLGvtMRINCELDVGLHRGGLSTa 194 marine gamma pr...
ZP_01307187  123 DILMGKPMPIQAVERFYQDgihn-------dfvAAQQIQWLVDSPQRLEQYREFAESNKlsMAINIELDVGLHRGGITRd 195 Oceanobacter sp...
EDY86751     115 DILLGKPMPIAAVKRFYKNltpe------qihsANRQIQWLVDGLEHLEEYRALAQSLNvtLRINLEIDIGLHRGGFKQg 188 gamma proteobac...
Feature 1                                  #                                                   ##
YP_957387    203 --gELARALTTIDh-sPWLSFSGFMGYEPHIMKAPgp----aaWLRDRAMARYRDYVSTAEQhlgr-sltDLTLNTGGST 274 Marinobacter aq...
ZP_01075537  206 --iIFEKMLKQIDa-dPALSFSGLMGYEPHVAKVPgs----klALRDAAMQSYRDKLAIALKisgk-htdELTLNSAGSP 277 Marinomonas sp....
YP_001189415 192 --qALGQALQHLQd-pPQLQLQGLMGYDAHVAHAApwt--eqrRVFADTNARYREFLAAARAfpll-wprQPLLNGGGSL 265 Pseudomonas men...
EAZ61229     172 --aALGELLALIAahpQHLEFAGFMGYDPFVGMGVpgilgspeELFAKVMALYQGHVDFARQrfaalwtpQLTLNTAGSP 249 Pseudomonas aer...
NP_900711    171 --aTLRRMLDMAAe-ePRLQWSGLMGYDAHVAKIPdlpg-lraKALRHARARYAAFAAAARAhpaartasGPCFNAAGSP 246 Chromobacterium...
YP_164851    157 ragEFAAALTRLRd-dPNLHLTGLMGYEPHIARLPrlia-sraRALDAARAAYARFHALTVQtlgagtaaKLIYNTGGST 234 Silicibacter po...
NP_108350    159 --eTLSKALSALPa-hKRLRCEGVMAYEAHAPHIPglfg-gpaKALAQGSDRAAAFVACLGAd------qRRILNIGGSK 228 Mesorhizobium l...
ZP_01754355  166 ---TLPPAIEAISt-lKGLRLQGAMGYEPHLAKLPa-------LLRAAARRRVESGLKLAREmlqv-hcnTPIINTGGSL 233 Roseobacter sp....
ZP_01615990  195 --qSLDAVLNIIDgdpEHLNFSGFMGYEPHLTGLKakl---esPSVQSVLSIYQAFIDQAKArgv--dteKLTLNGAGSH 267 marine gamma pr...
ZP_01307187  196 --sDLISMLDMIEt-sDTLNFSGFMGYEPHIGKVPgd----vlDHRDKAMAEYQHYVQLTEQhlkr-siqHLTLNAGGSP 267 Oceanobacter sp...
EDY86751     189 g-sDYPEALRYIHshtEYLALSGLMGYEPHIAKMPlasaermnKAKSKATAQYQWFKDYIKLnysdtyrtNLTFNGAGSP 267 gamma proteobac...
Feature 1                         ####                                                           
YP_957387    275 TYQLYrglsGELPVNELSAGSGLVMPTDFDLPTLAEHRPAAFIATPVLKLLEtt-rIPGAPGLGRLQALWNPNRARTAFI 353 Marinobacter aq...
ZP_01075537  278 TYRYYd--eGDYPHNEVAAGSCLVKPSDFDLDTLSDHEAAAFIATPVLKVMQdt-qIPGVDGLGRLMTIWNPNRSKTFYT 354 Marinomonas sp....
YP_001189415 266 TYPLHs--rSDTPLNEVAVGSALLKPGDFDTPALSEHQPALWIASPLLKVVDg--aLPYLGAVQPLMTAWNPNREHAYYL 341 Pseudomonas men...
EAZ61229     250 SYRMHe---KEMLSSEVSVGTAMLKPSHYDLASLAEHVPAVYIATPVLKSTGav-qIPALDGKSRLFSWWDPNQRGTFFI 325 Pseudomonas aer...
NP_900711    247 TYRLYh---GDGPENEVAVGSAMVKPADFDLPLLDDLLPACFIATPVLKTLPrfelPYGVEWLGGLVGGWDANARRGYFI 323 Chromobacterium...
YP_164851    235 TFMLYd---GSGPETELALASALVKPTDFDLPALEALQPAAFIAAPVLKTVErp-eIPMAPGLSRVLRLMGRSPERACFI 310 Silicibacter po...
NP_108350    229 TALLH----HGGIANEVSMGSAFVLPSDFDTAGLVGFQPAAFIAAPILKVVAp--mLPGPPAVTRLLQALGRFPRKGCYL 302 Mesorhizobium l...
ZP_01754355  234 TFDRYg---PQHGVSEVALGSLLVKPKDFGLPATEGFAPALFIATPVLKYMP----RNPIPGLEALSPLTGLRNRADLAI 306 Roseobacter sp....
ZP_01615990  268 TLGIYe---NDNLMNDLSAGSGIVKPMDFDTFYMKGNYPALFIATPILKRYDel-kLPGDPAIAKLLPLWNPNMQRLYYI 343 marine gamma pr...
ZP_01307187  268 TYQYYn--qGQWPMNELSAGSCLVKPTDFDLASLQDHEPACYIASPVIKQLDqa-eIPGIDFMGELLSSWDPNLKQAFFI 344 Oceanobacter sp...
EDY86751     268 TCQLYq---SDDTINDISAGSSLLMPTDFDLLSIRDQKPALFIATPVIKALGal-eLPFLEPICSLLARYNPNWQRSYFI 343 gamma proteobac...
Feature 1           #                                                                           
YP_957387    354 YGGNWPATPVSPAGLtDNPVYgRSSNQEMLNFAdgldLAEGDRVFLRPHQSESVFLQFGDLAIFdpaRGAITHRWPVFR 432 Marinobacter aqu...
ZP_01075537  355 YGGNWKAHPISPKGLsINPVWgHSTNQEMLNGSehiqLNTDDWIFLRPTQSEFVFLQFGNLIIYd--QEGIIDSWSVLK 431 Marinomonas sp. ...
YP_001189415 342 YGGRWPAHPVSPAGLdYDALYgRSANQERLIGSaatgLRADDWVFLRPAISEGLLGGFGEMRLLr--AGQLVGRWSTLP 418 Pseudomonas mend...
EAZ61229     326 YGGNWMADFASPEGLrSNGIYgRSSNQEMVNGSpsvgLEVDDQVFLRPTQSESVLLQFGDLLALr--GGRIVERWPVYA 402 Pseudomonas aeru...
NP_900711    324 YGGNWLADPASPSGLeSSGLYgHSSNQQLLVGSgrqaLAVDDMVFFRPRQSEAVLQQFGDIAVYe--GGRIVASWPVLP 400 Chromobacterium ...
YP_164851    311 YGGNWLADPCHPAGArRSALFgHSSNQEMYDLPanstLKPGDFLFFRPRQSEALFLQFGDIAVFd--GTAITDWWPVWH 387 Silicibacter pom...
NP_108350    303 YGGKWMAEPVFPEGMrTNGLLgLSSNQQFMGLPvdsvARPGDYAFLRPTQSEAVLQQFGPIAVFs--GGRIIDRWPVLP 379 Mesorhizobium lo...
ZP_01754355  307 YGGYWKASPVYPKDYgYSGIFgRSSNQEVWSGPrlkqSPVGGYAFLRPDQSEAILPEFGELLVVs--EQQELEHWPCFS 383 Roseobacter sp. ...
ZP_01615990  344 YGGYWKAKIVSPAGV-ADPIY-QSTNQSPITTSnsvdLQIDDYIFLRPTQSEHVMLQFGDILVVk--GGEIIDNWPVFH 418 marine gamma pro...
ZP_01307187  345 YGGYWKAKPESPKGLkLNPVYgRSTNQEMLNGSdsvqLKQDDYVFLRPTQSESVMLQFGDLLVYr--KGQLIDHWPILK 421 Oceanobacter sp....
EDY86751     344 YGGYWKATPCSPQGLsNNGLYgRSSNQELLTGSgssqLKINDVVFLRPSQSEAVLLEFGEILVVr--NNEIAEQWPHLA 420 gamma proteobact...

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