2VUG


Conserved Protein Domain Family
Adenylation_RNA_ligase

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cd07894: Adenylation_RNA_ligase 
Click on image for an interactive view with Cn3D
Adenylation domain of RNA circularization proteins
RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.
Statistics
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PSSM-Id: 185705
Aligned: 30 rows
Threshold Bit Score: 373.823
Created: 19-May-2009
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
active sitedimer interface
Conserved site includes 16 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:2VUG_A; Pyrococcus abyssi RNA ligase binds an ATP in the active site; contacts at 4A.
  • Comment:ATP-dependent DNA/RNA ligases utilize ATP as a nucleotide cofactor.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                      # ## #                   ####   #              #  
2VUG_A        48 RYVRFKDsagklRRGTVVIDe---EYVIPGFPHIKRIINlrSGIRRIFkrgEFYVEEKVDGYNVRVVMYKgkmLGITRGG 124 Pyrococcus abys...
O67191        25 EYLRFNDdykdiPRGTAIFK----DFIIWGYPHIGRIFLleTGLREQFe-aPFWVEEKVDGYNTRIFKYGdnyYALSRGG 99  Aquifex aeolicus
YP_001938667  24 SYVRLTHaykgwPEGTVFLK----DLAIAGFPKIGRINSlePGLREQFp-sSFWMEEKVDGYNVRIFQYKgkiLCATRGG 98  Methylokorus in...
YP_001435834   7 KYIHLKKgk-wgGKGSVIIYykgdVGVVPGYPSIQRLVLl-SKVPHYFp-eGVSVEEKMNGYNVRVVKVGgevFAVTRGG 83  Ignicoccus hosp...
ZP_01128873   34 RYIRIRTdyqgiPRGAVLVA----DRVIPDYPHIARVFAlaAGIRQSLs-gPFQVEEKIDGYNVRIFRVAdrcVAITRSG 108 Nitrococcus mob...
YP_001002560  25 DYVRLTDgfsgwPRGTVFLD----GRAVPGYPSIGRVLNleQGLAQHFr-aPFHAEEKIDGFNVRLVRHRgqdLAFSRGG 99  Halorhodospira ...
YP_743383     24 HYIRLHDsvarlPKGSVRLDd---GTVVPGYPSIGRIQAlgPGLAKQYgdeLFWAEEKIDGFNIRILAHQgrlLAFSRGG 100 Alkalilimnicola...
YP_003473574  25 EYLRFTDdfkdiPRGTILFK----ESVIWGYPHIGRIFQlsSGLREQFn-aPFFVEEKVDGYNVRIFYHEgqvLAVTRGG 99  Thermocrinis al...
ZP_05047997   35 IYYRLIDdsqpfRRGTVIFEe---GTLIPGYPQIGRMIRldKGLKEQFt-kPFWAEEKVDGYNVRIFLLGerlLGVTRGG 110 Nitrosococcus o...
YP_003461135  25 EYARLLEpvnhyPRGSVVLPd---GSVVPGYPSIGRIQSleAGLPRQFe-qPFWAEEKIDGFNVRILRWQgrvYAFSRGG 100 Thioalkalivibri...
Feature 1                                          #                        #                    
2VUG_A       125 FICPFTTERIPdf----vpQEFFKDN-PNLILVGEMAGPESPYLVEGPPyvkedIQFFLFDVQEIk--tGRSLPVEERLK 197 Pyrococcus abys...
O67191       100 FICPFTTDRLPdl----idLRILDEN-PDLVICAEVAGPENPYIEESPPyvkedVQLFVFDFMKKn--eQGFLSQEEKME 172 Aquifex aeolicus
YP_001938667  99 FLCPFSTDRIGel----mpLGIFNDH-PSLVLCGEIAGPDNPYIEGPSPlvqedIKLFIFDIAQLp--tLEFLPQRQKQE 171 Methylokorus in...
YP_001435834  84 YLCPYTNARLKsvyg-eelSSLLDELpPGSFVAGEVVGTENPYVRVEYPea-pkFDYFIFDIFVRegdgWRQMPVEERHE 161 Ignicoccus hosp...
ZP_01128873  109 RICPFTTDRLPdlldmtalERLFIEH-PDLILCAEVAGPGNPYMDMASPrggddVALFVFDLLRQg--qEQLVPLAQRDA 185 Nitrococcus mob...
YP_001002560 100 FVCPFTTDRLPdl----idPAVFQAE-PDLVLCAEVAGPGNPYLEGHPPeihedVALLVFDLMRWd--hAEFMAVEERRA 172 Halorhodospira ...
YP_743383    101 YLCPFSTDRVPel----ldPTLFDDH-PGLILCAELAGPENPYMEGSPPhvtedVALFVFDIRRAg--aNGFLPQEEKLA 173 Alkalilimnicola...
YP_003473574 100 FVCPFTTDRVEef----idADFFKEN-PHLVLCAEVAGPENPYVDESPPyiredIRFFVFDVMVKg--eQRFLPYRQKLQ 172 Thermocrinis al...
ZP_05047997  111 FLCPFTVDRLPdl----idERIFSDH-PDFILCGEIAGPENPYLIGSPPfikedIQLFIFDCQRKg--eFDYLSQAEKHQ 183 Nitrosococcus o...
YP_003461135 101 YVCAFSTDRVVdf----mdPVIFNAE-PNLILCAEIAGPDTPYLEGSTPrvahdVGLFVFDLMRLg--qPGFVSQPEKFA 173 Thioalkalivibri...
Feature 1                 #                               # #         #                          
2VUG_A       198 IAEEYGINHVEVFGKYTkdd--vdELYQLIERLSKEGREGIIMKSPDm-kKIVKYVTPyaNINDIKIGARVFYelPPGYF 274 Pyrococcus abys...
O67191       173 LIEKYNLPHVEILGRFTaseegikKIKEILKRFNEEGREGVVFKEDSernKRAKYITSyaNLMDIKTNAKNMLqlPPEYY 252 Aquifex aeolicus
YP_001938667 172 LICRYGLPSVKNFGLFKnngndlvEIKKILLCLHNEYREGAVFKEEPf-gRYAKYVTAhsDLNDIAVLSHKIMdiSPNYF 250 Methylokorus in...
YP_001435834 162 LVRRHGLRGVRLLGTFRpde-svsKIKEIVDRFDAEGREGVVLKDPLykrPPAKYTGSftNIGDIEQGMKYPFdeGKDYL 240 Ignicoccus hosp...
ZP_01128873  186 LLSHYGLPFPRHFGCFTvne--ltEVLEIVRHLDAEGGEGIVLKATLd-dRRVKYVCPsiNVEDVATEAALELelPGEFY 262 Nitrococcus mob...
YP_001002560 173 LLQEHGLPEVPYHGRFTvdq--agALRELIAGLDARGVEGVVLKEEGdrrKRAKYVTPasVVQDLGAMGDALLdlPPEYF 250 Halorhodospira ...
YP_743383    174 LAERYRLPLARVFGRYRadd--qqALHALILELDEAGCEGLVFKGETr-gARSKYVTArsNITDIALVSDALLdlPPEYF 250 Alkalilimnicola...
YP_003473574 173 LIEKYRLPSVERYGLYDvsk--igELKALLRRLNEEGREGVVFKEDSerdKRVKYITSyaNLQDIRITSLNLMglPADYY 250 Thermocrinis al...
ZP_05047997  184 LMEHYSLPSVRNFGLFKaed--ilAIKQLMMTLDTEGCEGLVFKEDVprgKRSKYVTSdaSLSDIQAMARYLPdfPPEYF 261 Nitrosococcus o...
YP_003461135 174 LIERHALPPAPLHGWFTprd--trALGELIRRLDEEGAEGLVLKTADg-qHRAKYVTGssCVSDIRVCAEQLLdlPPEYF 250 Thioalkalivibri...
Feature 1                                                                                        
2VUG_A       275 TSRISRLAFYLAEkrikgeefeRVAKELGSALLQPFVESIfdveqeEDIHELFKVRVkrIETAYKMVTHFEkl-gLKIEI 353 Pyrococcus abys...
O67191       253 TNRILRLVLFMYEeglk--tteHLYEELGRAFIDGLFQAIeqfekeHKVYKTFTCKFrkKENAIALLELLSkt-sKHIQV 329 Aquifex aeolicus
YP_001938667 251 IDRILRYVLFLIDmgii--eenGWDEKLGKAFISSIKEVLkrvkegGKSSRLFRCRFrnPQNAQYLIDHLKhi-pGHQEH 327 Methylokorus in...
YP_001435834 241 FPRIVREMFKVFEeglagrkleERALWLGRAILAPAVEAVkavaegRPLHEDFVLRFptEGDLEDYLDYVRql-gVKVTV 319 Ignicoccus hosp...
ZP_01128873  263 IHRVVRMVMALHElgqr-drihTLGPALGKALVSGFDQALhdmertHKISKVYRIRLrqEASIKALLDHIDqd-sRTISV 340 Nitrococcus mob...
YP_001002560 251 TNRLMRLVLILEEspel--dreTLRAELGAALIDPLLNAArehretHKVAHHFCSRFrhRANAERFAEHLRrv-pQSQIH 327 Halorhodospira ...
YP_743383    251 THRLMRLALFESEhrg---ddtALEQELGRALLRGLGRAVersrsvGRVGHRYRCRFreKRNLEHFVAHLEat-gGPQHV 326 Alkalilimnicola...
YP_003473574 251 TNRLLRLALFMEEeglq--leeDLLKELGSAFLEGIFEAIrqskeeGRVYRTFRCRFrkKESALLFMEQIQhs-sSQVQI 327 Thermocrinis al...
ZP_05047997  262 IGRILRSVIFLDEegis--sthELKAQLGSAFIDGLLKAIkqcqreHRVYHRFRCRLhdRANARQLLAHLArg-dGHIQI 338 Nitrosococcus o...
YP_003461135 251 TNRLTRLAIFLSEhpdr--hhaDLDQALGQALLSGLHGAVaqhrrqGHVGHRYRCRFreHASALRFMNHMRatggRHVSF 328 Thioalkalivibri...
Feature 1                                              
2VUG_A       354 vdie----eikDGWRITFKRlypdATNEIRELIgGKAF 387 Pyrococcus abyssi GE5
O67191       330 kerrl--ekegDYWRLEFDKvf-lNMTGLLGHLlSGGI 364 Aquifex aeolicus
YP_001938667 328 vivkk-fykdkDYWYLEFEKifpaTGDSLRNWLsGALR 364 Methylokorus infernorum V4
YP_001435834 320 lek-----weeGGWVVVKVRkfkrSPDVIESMLrTGRT 352 Ignicoccus hospitalis KIN4/I
ZP_01128873  341 qelar--erlgNHWELTFRKtfrrSTSKLETLLaGSPI 376 Nitrococcus mobilis Nb-231
YP_001002560 328 ttvrsleqaadGYWELRFDRvfprISGLLGNFLsGGQV 365 Halorhodospira halophila SL1
YP_743383    327 kilyqpthqedGYWVLEFERvlprMTGTLAHSLsGGAQ 364 Alkalilimnicola ehrlichei MLHE-1
YP_003473574 328 iergl--kqegSYWILEFDRvylnMTGFLGHVLgGGSV 363 Thermocrinis albus DSM 14484
ZP_05047997  339 vkhrl--vregEFYIFEFDKvfqrTTGLLGELLsGEMV 374 Nitrosococcus oceani AFC27
YP_003461135 329 aqdap--rqedGYWLLEFERqfdrITGTLASALaGDRQ 364 Thioalkalivibrio sp. K90mix

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