1DGS,1B04


Conserved Protein Domain Family
LIGANc
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cd00114: LIGANc 
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NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Links
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Statistics
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PSSM-Id: 238062
Aligned: 44 rows
Threshold Bit Score: 299.121
Created: 1-Nov-2000
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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Conserved site include 1 residue -Click on image for an interactive view with Cn3D
Feature 1:catalytic site [active site]
Evidence:
  • Comment:AMP is covalently attached to Lys as an intermediate of the proposed catalytic mechanism
  • Comment:Lys has been mutated to Ala in 1BO4_B
  • Structure:1DGS: AMP covalently bound to Lys
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                                                                                     
1DGS_A      8 RRINELRDLIRYHNYRYYVlADPEISDAEYDRLLRELKELEERFPEFks-------pDSPTEqvgar-pleptFRPVRHP 79  Thermus filiformis
1352291     6 LKIQQLVNLIKNYDYHYYVlSEPLIDDFEYDMLYKSLQQLEKDHPDLiq-------iDSPTQrvgge--avkgFKKLNHN 76  Mycoplasma genitalium
2494169     5 AQIRAIVEQLKRYDYHYYVlDDPLVSDFEYDQLYKQLQALEQAHPELiq-------pDSPTQrvggi--vveaFNKFPHQ 75  Mycoplasma pneumoniae
6899079     6 AKIDELKQKLDQWNYEYYVlDDPSVPDHVYDQTMRELIELENNYPQFkt-------nNSPSVkvggf--vsekFNKVKHK 76  Ureaplasma urealyt...
7673988     7 QEIADLKKLIRKWDKEYYVdSLPSVEDFVYDKHILRLQELESKYPEYkt-------lDSPTLkfgsd--llndFKEVEHS 77  Lyme disease spiro...
7674020     6 KEYLERIEYLNTLSHHYYNlDEPIVSDAVYDELYQELKAYEEENPNRiq-------aNSPTQkvgat--atneFSKNPHL 76  Helicobacter pylor...
NP_349280   9 LRMQELIEELNKYSYSYYVlDNPIVADKEYDKRYDELVELEEKTGITy--------pYSPTNrvgdv--ilkqFQKYTHK 78  Clostridium acetob...
NP_347827   2 KLIEDLIEKLNKYSYSYYVlDNPIVADKEYDIMYDELKRLEEETEYIn--------pNSPTQrvgdi--ildkFEKTHHK 71  Clostridium acetob...
NP_326220  10 SKIKELNEKLKLYNHHYYNkNESLVSDEYYDAKLLELENIRDNFPEEynqvfqkdfsKSVLEkvnhldeqdvkLKKEKHQ 89  Mycoplasma pulmonis
O83642      6 RRVQELEKLILHHQDRYYN-AESDISDDAFDALWEELARLDPGNPLLka-------iGSDSQr---------dAVKKRHI 68  Treponema pallidum

Feature 1                                                   #                                 
1DGS_A     80 TRMYSLDNAFTyeEVLAFEERLereae----------apslYTVEHKVDGLSV-LYYE-EGVWSTGSGDGe--VGEEVTQ 145 Thermus filiformis
1352291    77 SPMLSLENAFStkEIANFIDNInfqtn----------skneFVVEPKIDGVSIsLTYK-NGVLVHALTRGdgsVGEDVLN 145 Mycoplasma genitalium
2494169    76 NPMLSLDNAFDtaTIASFIANInnltg----------vqnrFVVEPKIDGVSIsLTYE-NGLLTRALTRGdglVGEDVLS 144 Mycoplasma pneumoniae
6899079    77 RPMLSLSNAFNddDLKKFDQDNqnasv----------dlkgYVVEPKIDGLSIsIIYK-NAKLHQAITRGdgiNGEDVTS 145 Ureaplasma urealyt...
7673988    78 APILSLDKVYDldLLKSWIDKIdfnn------------sfnISVEPKIDGCSIvLYYK-DGVLEKALTRGngkFGNDVTI 144 Lyme disease spiro...
7674020    77 MRMWSLDDVFNqnELRAWLQRIlkvy-----------pnasFVCSPKLDGVSLnLLYQ-HGKLISATTRGnglEGELVTN 144 Helicobacter pylor...
NP_349280  79 SRLWSLDKAQSfeEIIDWHNRNkkavaeynsnhedklpelkYVLTKKFDGLTInCTYDeSGVMIKAATRGtgvIGEDITS 158 Clostridium acetob...
NP_347827  72 NKLWSLDKAQKkdEVKAFVNKCvkfveqynlthseklpspqFVVTQKLDGLTInCSYN-ESRLIKSATRGtgeIGEDITE 150 Clostridium acetob...
NP_326220  90 KLMLSLNKAYSfeDLERYTNRIntfvg----------nnhqYILQEKIDGVSIsLYYE-NGILTKALTRGdgiYGENVTH 158 Mycoplasma pulmonis
O83642     69 VPMGSQHKAADeeSFSAWAKKNal---------------qaFLVQHKLDGVSLeLQYE-RGHFCCALTRGngiVGDDVTA 132 Treponema pallidum

Feature 1                                                                                     
1DGS_A    146 NLLTIPTIPRRLKg-------vPDRLEVRGEVYMPIEAFLRLNeelee----rgekvFKNPRNAAAGSLRQKDPRVtaKR 214 Thermus filiformis
1352291   146 NVKTIKSIPLTIPf--------TKTIEIRGEIFVDKKTFLAINnql--------ekpFANARNLAAGTIRNLNSEItaQR 209 Mycoplasma genitalium
2494169   145 NVKTIKSIPLTIPf--------HKQVEIRGEIFVDKKTFAQINenl--------akpFANARNLAAGTLRNLNSEVsaKR 208 Mycoplasma pneumoniae
6899079   146 NILTIKDIPHYIDqk-----ykDYEIEVRGEVYMAFHDFYEMNdnlee-----sdkkFANPRNAAAGTLRSLDNSIvaER 215 Ureaplasma urealyt...
7673988   145 NVRTIRYIPLFLDe--------KVDLVLRGEVYITKENFLKINkfl--------ekpYTNSRNLASGILRRVDSREvaNF 208 Lyme disease spiro...
7674020   145 NAKHIANIPHSIAy--------NGEIEIRGEVIISKEDFDALNkerln----aneplFANPRNAASGSLRQLDSNItkKR 212 Helicobacter pylor...
NP_349280 159 QAKTIKSIPLKIKn--------GSVVEVHGEAIMTKTAFNEYNkka--------evpLKNLRNGAAGALRNLNVREtaRR 222 Clostridium acetob...
NP_347827 151 QSKTILNLPNAINy--------SGEIDVHGEALMTKNALEQYNsnlkv-----netpLKNLRNGAAGALRNLNIKEtaRR 217 Clostridium acetob...
NP_326220 159 NALNIKDIPKTINi--------KENIELRGEIFFSLKLFESLKnefldkqdgtknkkWNTPRNKASGILKSLKTTDe-SS 229 Mycoplasma pulmonis
O83642    133 NVRGMRGFVPTLTaewgpcgnlPFTGGVRGEVIMHKDIHRSHYp------------tHANCRNTVNGILKRKDGRG--RT 198 Treponema pallidum

Feature 1                                                                                     
1DGS_A    215 GLRATFYALGlglgl----eesgLKSQYELLLWLKEKGFPVehcYEKALG---AEGVEEVYRRGLAQRHALPFEADGVVL 287 Thermus filiformis
1352291   210 KLRALFYYIPngl-------eesITTQTMVLEQLKQWKFPVsdtIRVFQN---KFQLINYLEAFDKKREQLTFNLDGLVI 279 Mycoplasma genitalium
2494169   209 KLKAFFYFVPnal-------tlgCRSQSAVLAQLKQWNFPVskaVASFDR---PEALIEYLEQFDQTRDQLNFQVDGLVV 278 Mycoplasma pneumoniae
6899079   216 KLSAFMYYLVnaq-------elgIKTHYESIQFLRDNKFKVsdlIVKVDT---INEVINQIDCYTKVRDKLSYMIDGIVI 285 Ureaplasma urealyt...
7673988   209 PLNIFIYDFLnag--------leFKTNDLATARLKKLGFKVnplIRFFDLknsIGEVLNYIADITKKRDSFEYEIDGVVL 280 Lyme disease spiro...
7674020   213 KLQFIPWGVGkhs--------lhFLRFKECLDFIVSLGFSAiqyLSLNKN---HQEIEENYHTLIREREGFFALLDGMVI 281 Helicobacter pylor...
NP_349280 223 NLSAFFYDVGyne-------gkaFKSYMEMMNFIKEMGFPVdeyLKECNT---IEEINKEIQYVGDIRSSLDYDIDGVVI 292 Clostridium acetob...
NP_347827 218 KLVAQFYDLSytd--------kkLKKYSEILLFLKSQGFNIt-eYNICNN---FDEINQAIDNIGEVRSSLQYDIDGVVI 285 Clostridium acetob...
NP_326220 230 WLSCFIYEVVspe-------nfnLKTQKQLFDFLKIQGFNLp-kFEFIEN---ENLIENFITNFKFEDDQRDYEIDGLVI 298 Mycoplasma pulmonis
O83642    199 HLHIVCYDAVpgtpgkpftgslpFADETEKLAWLARQGFVTv-hSHRCAN---AQEVVALRSEIMRTRELLPYSIDGLVV 274 Treponema pallidum

Feature 1                                 
1DGS_A    288 KLDDLTLWGELGYTaraPRFALAYKFPA 315 Thermus filiformis
1352291   280 KLNSLLFYQQLGATsksPRWAIAFKFSP 307 Mycoplasma genitalium
2494169   279 KLDNFHFYDQLGFTskfPRWALAYKFKP 306 Mycoplasma pneumoniae
6899079   286 KINNLEVYDEIGYTskfPKWAIAYKFPA 313 Ureaplasma urealyticum
7673988   281 KVSDFALRERLGYTahhPKWAMAYKFEA 308 Lyme disease spirochete
7674020   282 VVDELDIQKELGYTqksPKFACAYKFPA 309 Helicobacter pylori J99
NP_349280 293 VIDDYRTREYLGYTvkfPKWAIAYKFEA 320 Clostridium acetobutylicum
NP_347827 286 RLNDIETSRLMGYTikcPKYAIAYKFKA 313 Clostridium acetobutylicum
NP_326220 299 KLNDLSLYDLLGKTskfFHHSIAYKFRK 326 Mycoplasma pulmonis
O83642    275 KSTDLDFQDAQLPR---PKKQIAFKFST 299 Treponema pallidum

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