3WEV,2YMW


Conserved Protein Domain Family
LodA

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cd14732: LodA 
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L-lysine epsilon-oxidase from Marinomonas mediterranea and similar proteins
L-lysine epsilon-oxidase is responsible for oxidative deamination of L-lysine, producing L-2-aminoadipate-6-semialdehyde. Hydrogen peroxide is a side-product of this enzymatic reaction, which requires the cofactor CTQ (cysteine tryptophylquinone). CTQ most likely forms a Schiff base with the free amino acid substrate. The protein is also called marinocine, for its broad-spectrum antibacterial activity; the latter is most likely caused by hydrogen peroxide synthesis. The dimerization interface observed in the available 3D structure does not seem to be conserved. Homologs of LodA have been detected in various gram-negative bacteria, and they appear to be associated with the formation of biofilms.
Statistics
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PSSM-Id: 269832
Aligned: 27 rows
Threshold Bit Score: 688.3
Created: 18-Sep-2013
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active site
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1: active site [active site], 5 residue positions
Conserved feature residue pattern:x [CS] D C [QEH]Click to see conserved feature residue pattern help
Evidence:
  • Structure:3WEV: LodA from Marinomonas mediterranea binds the substrate, L-lysine; contacts at 4 A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                        
3WEV_A         1 MALSVHPSIGVARLGNanTDNFVLNPMEIGGLPYEHDvdlk----------------pttTVVNFKDEAGCIRRQGQVFK 64  Marinomonas med...
WP_009831693   5 LVFRVHPSINFARFGT--SDEYILSPETSAGLPQANDnvtgglpik------kdtesdpvTSNDLRDEEGFLRKQAARFR 76  Marinomonas sp....
NP_419374      4 PVFRVHPAIGIARVGN--SEEFYLGPETMAGLPVGPSvdtggrdldgglpiragtestiiSSDELRDSAGRMKRQAARFR 81  Caulobacter cre...
WP_017909911   4 NVFRVHPAIGIGRVGD--SQEFYLAPVTAAGTRGADGlmgglpvq-------pgtestpiTAEQFRDAAGNVKRQAARFH 74  Xanthomonas sp....
WP_006749250   4 TKLRIHPAIGFARVGS--SQEYYIAPETSAGMPIAGQaltgglpik------pgtentpiTSSDLRDAQGRLKRQAARFR 75  Burkholderia am...
WP_010558415   2 SYFRVHPSINFARVGN--SEEYYIAPETAAGTIVDKRtglfgglpi-----kpgtnntpiDEHDFRDSHGNVKRQAARFR 74  Pseudoalteromon...
WP_006513582   5 FIYRVHPAIGLARVGN--SKEFYLGPETIAGLPIPGCqanttgglpi----kpdtesetiTSRDLRDTQGALKRQAARFR 78  Leptolyngbya sp...
WP_008887301   1 MTFRIHPAIGIARVGN--SVEYYIGPETMAGMPQEGTdlngglpir------pdtdgetiTSADVRDGAGALKRQAARFT 72  Citricella sp. ...
WP_009599695   6 AVFRIHPAFGIARVGN--SEEFYLGPETMAGLPIAAGidtgnphvsgglpikpgteanviSSEDLRDRSGRMKRQAARFR 83  Xanthomonas tra...
YP_004989740   4 SSLRIHPAIGMARVGN--STEYYLGPETMAASPHGASaitgglpik------pgtesthiTSGDIRDGSGRLKRQAARFK 75  Owenweeksia hon...
Feature 1                                                                                        
3WEV_A        65 VFGAs-------------NEELTLDSp-----nVKNIEWTVHLANKKAAWYEFRELNGNLLYgrdnsysa---------- 116 Marinomonas med...
WP_009831693  77 IYAYengkse---ypsgeGTEVTIGTvlpdgrkVKTMLWSCHLANKKSAAYNVVNDKGIKAYddgvpqr----------- 142 Marinomonas sp....
NP_419374     82 IYHYpdqtggkerypcgqGEEIVIGSvvg-grtVTDIVWTVHLANKKANSYMLNDMLGMQVYdkahasdlh--------- 151 Caulobacter cre...
WP_017909911  75 IYAYpsgssg--sypnggGVRVDVGStid-gktVKDIVWTVHLANKKLNNYSTVSQGGQFRGigayeepgvlel------ 145 Xanthomonas sp....
WP_006749250  76 IYQYddaalt--rypsgsGTEVVIGSsvd-gkvVKDIVWTVHLANKKANCWVLESTPAGLPAyendkhppi--------- 143 Burkholderia am...
WP_010558415  75 IFAYddeqtt--ypsndgGREINIGDnig-gkvIKDIIWQVHTANKKNNNFTITSIVDGEPQeegviayqnen------- 144 Pseudoalteromon...
WP_006513582  79 IYQYttqdqd--kypsgaGTEITIGStin-gqkVVDMIWTVHLANKKANNYVLENPRLGTFNkiidgykeggl------- 148 Leptolyngbya sp...
WP_008887301  73 VFEYddaplg--sfpsgdGTPVGIGTvlsdgrtVTDIIWTVHLANKKANCWLEVDEEGIASYtggglpplr--------- 141 Citricella sp. ...
WP_009599695  84 IYHYpanasa--gypsgaGSEIVLGTdvd-gkrVRDIVWTVHLANKKANAYMLNDELGLAVYeaanaerlh--------- 151 Xanthomonas tra...
YP_004989740  76 IFQYpnegekl-typtqgGEEVLIGStvd-gkkVTDIIWTAHLANKKANCWEIDEDANKGIElykphppiddktitklvs 153 Owenweeksia hon...
Feature 1                                                                                        
3WEV_A       117 ------------rgvpwrnaSKTASSERQSLIIDLGPRSVSgv-----mATVEIs----------------iNNIPETYl 163 Marinomonas med...
WP_009831693 143 -------------rnpevhgDINDPNRLNQLMIDPGPRVIN--------GRRQSsvgfnastpaefvnnkgeVTELPDY- 200 Marinomonas sp....
NP_419374    152 ------------lrnaaegdDLNNAARLRRLVIDAGPRAIRgae--akaVRFDKatiash------atldaaIETLPHY- 210 Caulobacter cre...
WP_017909911 146 --------rnpdypgaadpaDPNDPTRLRQLVIDPGPRALSaaaagsavVGFDMtttasy------adasgtIHPQPAY- 210 Xanthomonas sp....
WP_006749250 144 -----------rnagfastsDPSNRTRLQKLVIDAGPRAIKasv--ggtVAFDKntrasy------gassgdVVDVPRY- 203 Burkholderia am...
WP_010558415 145 ---------tppvrnpkfgdDLNTVMRRQQLVVDPGPRALSvtsnsntcLSFDKktpdsf------ieegkiATAASCY- 208 Pseudoalteromon...
WP_006513582 149 ----------pplrnpdegpEASSFDRLRKLVIDPGPRAIKgtd--tdaIHFDKcttasf------gpgnseIRSLPDY- 209 Leptolyngbya sp...
WP_008887301 142 ------------npgfggadDPSAPERLAKLVIDAGPRTIQgtg---asVEFDTatpasa-------yvggaVTELPDY- 198 Citricella sp. ...
WP_009599695 152 ------------lrnaaegaDPDNAARLKKLVIDPGPRAIRgtq--pqsVRFDKatvasf------asaaatIETMPYY- 210 Xanthomonas tra...
YP_004989740 154 tpplrnpnfdstspqnpynvDPGDTNRLKKLVIDAGPRAIKasqg-tkpIKFDDepkasyy-----dkssgtITDLPNY- 226 Owenweeksia hon...
Feature 1                                                                                        
3WEV_A       164 HPSYPSGEllq-----gskHFESLGTLRTDSQ-GRLIVLGGYGFAGGn----------------tDLSGYGGGDDWYDDI 221 Marinomonas med...
WP_009831693 201 PIRFPQDTneklf--epsgPLNTLGEMRTDGM-GRLLLLASSGNAVGqydey---------dqviQMNGDLNNAGWFDSA 268 Marinomonas sp....
NP_419374    211 PKTFPDDSfarmy--tptgGIETLGELRTDQH-GRLLVLPAWGRAAGwlqadgtpfplvggliapGEYGDVNADGWFDDT 287 Caulobacter cre...
WP_017909911 211 PVSFPSMFhtlh---eplgKLDSLGDMRVEAN-GALIVAGGFARTSAvigad---------gsypPLEDATENGLWYDDA 277 Xanthomonas sp....
WP_006749250 204 PMSFPASNvaslppasgctPITTLGAMTTEPN-GRLLVLGASGLACGfdadgr-------atadaALGGDVDNDNWLDDT 275 Burkholderia am...
WP_010558415 209 PKSFPDDFfymf---nplgEISSLGEMRIEENtARLIVTGGFGKASGilgnksdk---dkkccipKLNGAIDNDDWFDDT 282 Pseudoalteromon...
WP_006513582 210 PTSFPSDSfdrly--spvgDIDTLGELRTDSH-GRLLVLAAYGRACAwypdnd------qgaspyALSHDVDNNGWFDDT 280 Leptolyngbya sp...
WP_008887301 199 PKQFPDTAtfpdlvcpsgeAITTLGGLRTDSK-GRLEVLGGHGLACGfga------------nalPLTHDVNNDGWFDDT 265 Citricella sp. ...
WP_009599695 211 PKSFPDDGfsqly--tpvgKIETLGELRTDEQ-GRLLVLPAWGRACGwlqadgtpfpliggliapGEYGDVNADGWFDDT 287 Xanthomonas tra...
YP_004989740 227 PIQFPATNgsga---ngsdPISYLGEILTEPN-GRLLVLGGHGLACAfdnqgn-------fdaeqPLCKDVDNDNWLDDT 295 Owenweeksia hon...
Feature 1                                                                                        
3WEV_A       222 SDGSVTCVVTYSDD--SSETSTAWMVVGSPDFAPEIVNISTLSDTCFDVGVRNFDLVPDMYdsatghykSDYVANFDRDI 299 Marinomonas med...
WP_009831693 269 ADGPVDVTLVFEDDs-IEQVHGAWVVCCDPAYAPQIRNVVSVWDNLYDMFVRKLSLQPDLYdqasdkynCEYTPSFTQDI 347 Marinomonas sp....
NP_419374    288 GDGPVSARICFDDGa-VVEAAQAWAITTDPSYAPQTLNVISLWDDMYDTWVRKLDLVPDLFdhr---fnTEFAPLFDDHL 363 Caulobacter cre...
WP_017909911 278 ADGPVNAVLIFNDGs-TASVQGAWYVTGDPGYAPQTRNVVSTWDDVYDVWVRALGLVPSLYann--afvATYQPSFSDDI 354 Xanthomonas sp....
WP_006749250 276 GDGPVTAWIVFSDGsvRAADSSAWVVSTDPAYAPQTRNVVTLWDEILTMWIETFQLRPDIHngl--ayrQDFRPSFDEHV 353 Burkholderia am...
WP_010558415 283 SDGPVTATIVFDDGs-FEEAVHGWFVCTDPSYAPQTRNVVSTWDDVYDTWIQHLALAPNIFdng---fnHDHLASFDGDV 358 Pseudoalteromon...
WP_006513582 281 SDGPVSVVLVLADGs-TQSVHGAWAVATDPAYAPQILNVVSLWDDIYNSWVQEPALAIAPQlfangefnPNYQPSFEDEI 359 Leptolyngbya sp...
WP_008887301 266 SDGPVTAVLVLDDGseVPLEGSAWAVATDPGYAPQTLNIVSLWDDIYNTWIEHFDVNPGIYang--aylPDYQPDFYEDI 343 Citricella sp. ...
WP_009599695 288 GDGPVSALLVFEDGs-TAEVVPAWAIATDPSYAPQTLNVVSLWDDMFDTWVRRLELAPTIFkyr---fdPAFKPSFADHL 363 Xanthomonas tra...
YP_004989740 296 SDGPVTAVLVFEDGsqQPVEGSAWAVVTDPAYAPQTLNVVNLWDDVYNTWLENFDLQPEVYsng--nynPDYKPFFQDDI 373 Owenweeksia hon...
Feature 1                                                                                        
3WEV_A       300 LPIIQRISQYQWVSNVQSMSGffsfqfDYRDg------SAANKANRMKYYNYFRQLDnkvigdydQPQQVLmssevegdi 373 Marinomonas med...
WP_009831693 348 KPIFIACNLQRWTANLPPFALna---hTAVDa------IDAKDDPNKTIMSGLNFIR--------NPNKDEsni-----g 405 Marinomonas sp....
NP_419374    364 KPIFRAPALQRWNTNLPSRAIaa---hDAVAai---aaGDKPGDTIMTGLAYVRDPN--------NPEQTNig------- 422 Caulobacter cre...
WP_017909911 355 QPIFHAAMLQRWNTNLPSGAVkg---hDMIGqi---qpTDDPSAKIPNLKTLIRDPAs-------AADTETg-------- 413 Xanthomonas sp....
WP_006749250 354 FPILRAASLQMWNTNLPAKAMks---hENID-------KLTAAKPPFDIMSFIRSPHp-------DSPSSTvg------- 409 Burkholderia am...
WP_010558415 359 QPVFHGAFLQQWNTALPEKGI------QGHKrmkeikpSDTPSEKIPSFTSLLRKPSapg--tkdEPNNEDgt------- 423 Pseudoalteromon...
WP_006513582 360 NPIFQAASLQMWTTNLPQRAIra---hHAVGei---kaSDKPSETILAGLAFIRNPN--------NPSESGvg------- 418 Leptolyngbya sp...
WP_008887301 344 FPVFRAASLQMWNTNLPDSAIaa---hDSIDni----tPEDDPGNRLYVKALIRNPNp-------DPDGSNdfa----tg 405 Citricella sp. ...
WP_009599695 364 QPIFRAPALQRWNTNLPQRAVaa---hDAVGki---aaQDAPSGTIMTGLAYVRDPN--------VAAQSNig------- 422 Xanthomonas tra...
YP_004989740 374 FPTLNAAHMQMWNTNLPDQAI------SAHE-------RMKLLTEEKPPFDIMKFIR--------NPDDSQndk-----g 427 Owenweeksia hon...
Feature 1                    #                                                                #  
3WEV_A       374 lPLMPMNSGSNSVsssnfydltdnvveKFLALDATQLFLLGQWAEGEFTAGPAd---dYPVSDMDTASIGNCVGLPMCPG 450 Marinomonas med...
WP_009831693 406 aPLMPLSLGEAGT--------------SFLTVTKTQYFNLEQWSKNSFSQDEGsk--lGKGELLDIASLSNCLGGRYVPG 469 Marinomonas sp....
NP_419374    423 aPFMPLSMGDAGK--------------AFLTVTRTQYFFLEQWDQGRFKPDATlt--fGPGEALDRIVLVNCLGGRFAPG 486 Caulobacter cre...
WP_017909911 414 sPMMPLSLGDAQK--------------SFLSVSSTQYFLMSQWHGKNYVQGGApv--lGPGEALDRVTLQNCLGGRYSPG 477 Xanthomonas sp....
WP_006749250 410 sPLMPLALGDNQR--------------SFLTLTDAQYFFVNQWANGMSEQATPas--yGPGEALDRIVLSNCLGGRLSPG 473 Burkholderia am...
WP_010558415 424 rKKMPLALGDAMK--------------SFLSVTETQYFLLMQWYNNKFNATAPs---lGEGEQLDKVVLENCLGGRYSPG 486 Pseudoalteromon...
WP_006513582 419 aPLMPFHLGDQGQ--------------ALLSPTFTQYFFLSQWDKEQFVPGANaltalGPGEYLDKAILMNCLGGRFSPG 484 Leptolyngbya sp...
WP_008887301 406 sPLMPLSLGDAGK--------------AFLTLSTSQYFFVMQWFDKKFTATPPvp--lGPGERLDKVVLANCLGGRFSPG 469 Citricella sp. ...
WP_009599695 423 aPFMPLSMGDAGK--------------AFLTVTQTQYFFLKQWNRGDFDAEATva--fGPGEYLDRAVMVNCLGGRFAPG 486 Xanthomonas tra...
YP_004989740 428 aPLMPLSLGDSNQ--------------AFLTVSRQQYFYMQQWNKGMSVGASKlp--iGAGEQLDKTILVNCLGGRFSPG 491 Owenweeksia hon...
Feature 1                                                                                      # 
3WEV_A       451 IEMTWSLQNPVIYKDAYQIkhyqdkayfdvng-----------------ltperdeceeetGCEPGDLTKRMACPWQADF 513 Marinomonas med...
WP_009831693 470 IEVSYSIMDKEIYIQDWRKsgagpfrikhkrmdyqgln-----kadpylnigwiprhgmtdGLEPGDLSKFMAIPWQTDY 544 Marinomonas sp....
NP_419374    487 IEATFVMRDPSIYQADWETsgggpfrlrarrldysqvqasqpfltvgyipmhpgpdgirpaPMEPGDVTKFMAVPWHTDY 566 Caulobacter cre...
WP_017909911 478 IEVSFPIRDVNLYVQDWKAqdcgpfrinqapldyska-------nqgsaflsfgyvplqqhLVEPGDLSKFMSVPWHTDY 550 Xanthomonas sp....
WP_006749250 474 IDLTFIVRDPNLYNPSWSAdhavgpvvgpfrinmrqldy--ttvsanqpflgvgyfprrdaKVEPGDLCKFMSIPWHTDY 551 Burkholderia am...
WP_010558415 487 IDLTFIVRDTHLYKTDWHGktgpfrinmatldyska--------tqnepflqvgyiplrdsKVEPGDLSKFMSQPWHTDY 558 Pseudoalteromon...
WP_006513582 485 IDMTFIVRQPEVYQTDWREtgagpfrlkakplayteat-----taqpflsegyvpyhsasdGLEPGDPSKFLANPWHTDY 559 Leptolyngbya sp...
WP_008887301 470 IDLTFIVRDTELYNSDWTNpaigpfriamapldygsaq-----agtpflgvgytptrpgqaGVEPGDICKFMAIPWHTDY 544 Citricella sp. ...
WP_009599695 487 IEMTFVIRDPSLYRADWQSsgygpfrirarpldyanvqysqplltvgyvpyhpgpdgigsaPVEPGDLSKFMAVPWQTDY 566 Xanthomonas tra...
YP_004989740 492 IDLTFIVRDPNLYNKDWQNpaigpfringesldyasa-------tkdqpflgigyiplrsdPVQPGDLCKFMSIPWHTDY 564 Owenweeksia hon...
Feature 1          #  #                                                                          
3WEV_A       514 FNCTIQTVNFsepsvnkasqtetvtsrthyewgnlpagvsvpdqssvsatknvdekvplppaYYSYWXPPQSPWDVLTGe 593 Marinomonas med...
WP_009831693 545 NSCSIHATAIntdgvnm---------------------------------------sngaesTLYWSWPSQRPDAVYVAe 585 Marinomonas sp....
NP_419374    567 NACATHNSAPnpt----------------------------------------------nstALYWSWPAQRPVQVHVAs 600 Caulobacter cre...
WP_017909911 551 NSCATHLPDPnpgqqt-----------------------------------------vnpnnTLFWSWPAERPFAVYPAa 589 Xanthomonas sp....
WP_006749250 552 NSCATHLPSPnpgaeikpdg---------------------------------snvysgvntTLYWSWPAQRPVAVYTYd 598 Burkholderia am...
WP_010558415 559 NSCATHTPDPnptmpnpng-----------------------------------egeaiadnTLYWSWPAQRPVTVYPKf 603 Pseudoalteromon...
WP_006513582 560 NSCATHQTAPnppspl----------------------------------------mnqpssTLYWSWPSQRPVAVYPAa 599 Leptolyngbya sp...
WP_008887301 545 NSCATHLPEPnpggdvnsrk--------------------------------dphvfegintTLFWSWPAQRPVAVYTFd 592 Citricella sp. ...
WP_009599695 567 NACATHNSAPnpd----------------------------------------------dssALYWSWPAQRPVAVHVAa 600 Xanthomonas tra...
YP_004989740 565 NSCATHTPAPnpggkitdk----------------------------------nvysgtvntTLFWSWPAQRPVAVYTFd 610 Owenweeksia hon...
Feature 1                                                                                        
3WEV_A       594 ldtegqlhs---------------------------hlpagqqinyARGINSYsQMVEHWSALAFIRDRNqnn------- 639 Marinomonas med...
WP_009831693 586 evinnvlpqqkws--------------------vrgpgtyainpasAATFQNPvQSVTDWDKIGFIIQGTniddk--ykq 643 Marinomonas sp....
NP_419374    601 dvhngklgpqrys--------------------vrgpgttsddlgeTGRFQDLvDIVRYWHRIGFIVQGTaidgd---eh 657 Caulobacter cre...
WP_017909911 590 lcqvdpdddtwylgpq--------------vysvrgegtdspyptrAGRFQAYaDFVANWSKVGFVISGAqiaqvsgkpp 655 Xanthomonas sp....
WP_006749250 599 dlvanhgelpvqryslrge--------gtaaiqqdstrefnsppmnVGRYQNRrDFLLNWDKIGFVIQGVaidry--dss 668 Burkholderia am...
WP_010558415 604 lfkydantgqgkgvsly------------svrgdeghgtktfypqqQGRFQCYfDFVENWHKVGFVIQGLqinddstkqn 671 Pseudoalteromon...
WP_006513582 600 dvnsdhqlpenary------------------smrgkgtqstnpenQGRYQNRlDILPNWHRLGVVIQGSaids----gt 657 Leptolyngbya sp...
WP_008887301 593 dlaanggalprqkfsvrg---------egtkaqpspagpgpfpaqnVGRFQDReNILLNWQKIGVVMQGPaidgy--dps 661 Citricella sp. ...
WP_009599695 601 dvrdgalgaqrys--------------------irgagtasddlgnAGRYQNLiDIVLNWQRIGFVIQGSaiagd---ir 657 Xanthomonas tra...
YP_004989740 611 dlsanngdlkatkqrysvrgegtaaqenlktpdcpdskefdtaamnVGRYQNRrDILTEWVKIGTIIQGPaikdy--pde 688 Owenweeksia hon...
Feature 1                    
3WEV_A       640 dgFPFFTETERN 651 Marinomonas mediterranea MMB-1
WP_009831693 644 ydANLYLEVEGQ 655 Marinomonas sp. MED121
NP_419374    658 ydREMFLEVQGQ 669 Caulobacter crescentus CB15
WP_017909911 656 ypAELFLEVASQ 667 Xanthomonas sp. SHU199
WP_006749250 669 ypPNYYLEVQSL 680 Burkholderia ambifaria
WP_010558415 672 ygPDYFLEVASQ 683 Pseudoalteromonas spongiae
WP_006513582 658 ysQEHYLEVASQ 669 Leptolyngbya sp. PCC 7375
WP_008887301 662 ypTNYYLEVASL 673 Citricella sp. SE45
WP_009599695 658 ysPDMYLEVASQ 669 Xanthomonas translucens
YP_004989740 689 fsKDYYLEVESL 700 Owenweeksia hongkongensis DSM 17368

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