1L1L


Conserved Protein Domain Family
RNR_II_monomer

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cd01676: RNR_II_monomer 
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Class II ribonucleotide reductase, monomeric form
Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). Class II RNRs are found in bacteria that can live under both aerobic and anaerobic conditions. Many, but not all members of this class, are found to be homodimers. This particular subfamily is found to be active as a monomer. Adenosylcobalamin interacts directly with an active site cysteine to form the reactive cysteine radical.
Statistics
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PSSM-Id: 153085
View PSSM: cd01676
Aligned: 6 rows
Threshold Bit Score: 875.301
Threshold Setting Gi: 22298870
Created: 7-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
putative active
Conserved site includes 5 residues -Click on image for an interactive view with Cn3D
Feature 1:putative active site [active site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                     
1L1L_A     27 GWVTYKRTYARWlpek-grsENWDETVKRVVEGNINLdprlqdsp--slelkqsLTEEAERLYKLIYGLGATPSGRNLWI 103 Lactobacillus leic...
Q2PDF6     94 GEVVYLRTYAREkdn--gqsEVWLDTVQRVVTGTFEVlqhhvvnklhchwdaqkAKERSEDMFRRIFEMKFLPPGRGLWA 171 Euglena gracilis
YP_007110   8 AMATALRTYHRPvkegdtqlENWDQVVERVISHQRWLweralg-----rtlneaQEDELEEIRSLISNRQIAPAGRTLWL 82  Parachlamydia sp. ...
A6Q367     30 SEVTFYRSYSRLked--gtnEHWPDTVIRVTEGIFSIrknhalny-hlpwdeeqAQIFAKEFALSMLQLRWLPPGRGLWM 106 Nitratiruptor sp. ...
XP_629553 100 GEIVYRRSYSRVked--ntnEQWFETVERVVNGTYNIqrkwierh-glewnqnkAQKSAQEMYNRIFEMKFLPPGRGLYS 176 Dictyostelium disc...
NP_682117  19 AYPVFYRTYSRQnea--gerESWQQVCDRTLKGLQEVgh--------------lTEAEVALLREMQEALKALPSGRWLWV 82  Thermosynechococcu...
Feature 1                      #                                          #                   
1L1L_A    104 SGtdyqr--rtgdsLNNCWFVAIRpqkygdskivpsylgkqekavSMPFSFLFDELMKGGGVGFSVARSNISQIPrvdfa 181 Lactobacillus leic...
Q2PDF6    172 MGspicrkkgfaaaLNNCAFVSTAtle---------------kdrVGPFLFLMDASMLGVGVGFDNAGAGSFTVPgpdd- 235 Euglena gracilis
YP_007110  83 GGtelsr--tressMFNCSYTHVEt--------------------VYDVVDVLWLLLQGCGVGFRPITGTLNGFRrplqe 140 Parachlamydia sp. ...
A6Q367    107 MGtrymye-rgsagLYNCAAVDTSn-------------------lAHAAEWAMDMLMVGAGVGFNTAWSGKATKPdkk-- 164 Nitratiruptor sp. ...
XP_629553 177 CGsstteskglfaaLNNCAFVSTLdik---------------knpSKPFIFLMDASMLGVGVGFDTKGENSIIIKgqlpp 241 Dictyostelium disc...
NP_682117  83 GGtdwvrqpenfsgAYNCTSTNVVd--------------------WDSFGLMMDLAMQGCGTGAILEPKYISQLPaicnr 142 Thermosynechococcu...
Feature 1                                                                                     
1L1L_A    182 idlqlvvdetsesydasvkvgavgknelvqdadsIYYRLPDTREGWVLANALLIDLhfaqtnpdrkQKLILDLSDIRPYG 261 Lactobacillus leic...
Q2PDF6    236 ------------------------------tqptYKFMIPDKREGWVESLKRLLKAhfc-----htADVEFDYSKIREMG 280 Euglena gracilis
YP_007110 141 ikvirsnrtek-------ggiqnnvetydpethiWTIKVGDSAIAWAKAVGKLVAGkf------paQTLVLDFSEIRPAG 207 Parachlamydia sp. ...
A6Q367    165 --------------------------------hpKIYVIDDSKEGWVKSVRLLIQSytd-----ngPFYRFDYSKIRPAG 207 Nitratiruptor sp. ...
XP_629553 242 pppqqqp----------------qqqqqqhgqnnNIFIVPDSREGWVESVQLLLDSyfl-----krNNPIFDYSSIRKKG 300 Dictyostelium disc...
NP_682117 143 levtvvgeigqt-----prearqehttvtltgqtCQIKVGDSRQGWVKSYQTLLELasnph-lgglVQVTIDIRDVRPTG 216 Thermosynechococcu...
Feature 1                                                                 #                   
1L1L_A    262 AEIHGFGGTASgpmPLISMLLDVNEVLnnkag-grltaVDAADICNLIGKAVVagnvRRSAELALGSNDDQDFISMKQDQ 340 Lactobacillus leic...
Q2PDF6    281 TKLKTFGGTSSgpgPLINLHKSIRKILvgekg-kpisvTCITDIMNLIGVCTVagniRRSAEIAFGEADCKEFLDLKSYE 359 Euglena gracilis
YP_007110 208 TRLKGYGWISSgdeQIAKAFKAIAKILsdrsd-qlltrMDILDIVNWLGTILSsrrsAQIALFEYDQPEWEDFAIAKKEW 286 Parachlamydia sp. ...
A6Q367    208 SPLKTFGGIAPgpePLKRLHKKIEQILddyldkkidktRCVVDLFNNIGLCVVsgniRRSAEIAIGRPGDKTFLHLKDYE 287 Nitratiruptor sp. ...
XP_629553 301 EPIKGFGGVCCgyePLKELHDEIRALLnkcig-kpissTNIVDLMNLIGKCVVsgnvRQAAEIAFGDPNSQEYIDLKNYQ 379 Dictyostelium disc...
NP_682117 217 ERLKGFGGVANp-vKLPHLYHRCAALLnaavg-rqltsVECCLLIDEAAVVVVagnvRRSAGMRQGASEDEAFAQAKQNL 294 Thermosynechococcu...
Feature 1                                                                                     
1L1L_A    341 eklm-----------hhrwASNNSVAVDSAFs----gYQPIAAGIRENGEPGIVNLDLSKNYgrivdgyqa--------- 396 Lactobacillus leic...
Q2PDF6    360 tnphr---------veygwASNNSIFAKVGMd-----YSDACERVRTNGEPGFAWLSNMQAFsrmngkpd---------- 415 Euglena gracilis
YP_007110 287 wikgn----------ahrqQSNNSLLFRSKPnreeleRVFQLMLDSGGSEPGIINAAEAERRapw--------------- 341 Parachlamydia sp. ...
A6Q367    288 kfper---------keygwISNNSVVIENLDdf--hyIDAITSLIASNGEPGVLHLENMQKYgrfgeiv----------- 345 Nitratiruptor sp. ...
XP_629553 380 inpqr---------asfgwCSNNSVFAELGMd-----YSKVCQSILHNGEPGLAWLDNMKAYsrmvpteld--------- 436 Dictyostelium disc...
NP_682117 295 wqqdaqgnwridpkrdalrMANHTRVFHRKPsl--eeCINAVRSQFYSGEGAIQWAGEAIARanadllttphlkqaflra 372 Thermosynechococcu...
Feature 1                                                   #                                 
1L1L_A    397 ----------------------gidgdvegTNPCGEISLanGEPCNLFEVFPLIAeeqgwDLQEVFALAARYAKRVTFsp 454 Lactobacillus leic...
Q2PDF6    416 ----------------------yrdqrvlgGNPCLEQSLesMELCCLVETFPDKHet-leDFKRTLYSALLYAKTVTLlp 472 Euglena gracilis
YP_007110 342 ---------------------------fkgCNPCVEILLgnKSFCNLTEVNVLAFrgdkvGLERALYLAGRMNYRQTMvn 394 Parachlamydia sp. ...
A6Q367    346 ------------------------pdrawlSNPCGEIALesYELCNLSEIFISKCsn-eeDFQKLIEYATFYASTVNLlp 400 Nitratiruptor sp. ...
XP_629553 437 ----------------------ykdrramgGNPCLEQTLesYELCCLVETFPNNHes-leDYLKTLKYAFLYAKTVTLgs 493 Dictyostelium disc...
NP_682117 373 yenqqgeaflrqllpamdqrelahrlgrygLNPCGEIIGa-DFHCNLAEIHLNQIdpadtATQEKAFKAGALSVAALLnh 451 Thermosynechococcu...
Feature 1                                                                                     
1L1L_A    455 yd---weiSREIIQknRRIGISMSGIQDWLLTRLgnrvvtgfkddfdpetheaikvpvyDKRAIKMVDQLYKAVVKADqd 531 Lactobacillus leic...
Q2PDF6    473 lh---wreSNEIMLrnRRIGCSVSGIAQFITNRG-------------------------LHELKTWLEEGYDILHQYDcq 524 Euglena gracilis
YP_007110 395 lr---deiLQEAWHl-NNDFLHLCGVGLTGVRARpd---------------------ltAYDFKRMRNITVSAAYSMAne 449 Parachlamydia sp. ...
A6Q367    401 th---rpeTNEIIArnRRIGVSVSGVADAIEKFG-------------------------LETIIKWLRKGYEKVRTVNer 452 Nitratiruptor sp. ...
XP_629553 494 tq---wpdTNKVLLrnRRIGCSMSGIAQFIHFNG-------------------------LHQLKDWCVNGFKLLNELDek 545 Dictyostelium disc...
NP_682117 452 rfvveryqYSRAID--PIVGVSFTGLFDFFVHAFgvpwlewwaagrpdtpqgrqfknqeAAFLQRWRQIVHETVWQYCdr 529 Thermosynechococcu...
Feature 1                     #                                                               
1L1L_A    532 ysktlgcneSIKHTTVKPSGTVAKLAG------ASEGMHFHYGAYLIQRIRFqdSDPLLPALkacGYRTEAdiyt----- 600 Lactobacillus leic...
Q2PDF6    525 isewlcirqSIKLTSVKPSGTISLVAG------ATPGVHYPESCYYTRRLRMarDSPLLERLikaGYHVEPccva----- 593 Euglena gracilis
YP_007110 450 ln----splPKNVTCIKPSGTISKIMGteewgeVPEGIHMPLGKYLFNNITYskHDPLVTKFraaGYTVIEkpye----- 520 Parachlamydia sp. ...
A6Q367    453 lakeagipvSLKVTCVKPSGTISILAG------TSPGMHYPLATYALRRIRIgkTSKLAKLLidsGLSFEEdiyd----- 521 Nitratiruptor sp. ...
XP_629553 546 ysewlaipkSIKRTSIKPSGTVSLLAG------ATPGMHYPISEYYIRRIRIqkESNLIPPLveaGYHVEPafen----- 614 Dictyostelium disc...
NP_682117 530 hg----lkrPNRCTTVQPSGTKSLLTG------ASPGWHPPKAQRFIRRITFrkGDPVAMACydyGYNVIPsqsdkdetg 599 Thermosynechococcu...
Feature 1                                                                                     
1L1L_A    601 ----------entTCVEFPIKAVGADnpnf-----------asagTVSIAEQFATQAFLqtYWSDNAVSCTITFQDs--- 656 Lactobacillus leic...
Q2PDF6    594 ---------pdvtAIVEFPVAAGNSIrt---------------trDITMWEQLSLAAFMqrYWADNQVSATITFDPe--- 646 Euglena gracilis
YP_007110 521 ----------pesVLVKFPVKFENVPftrttvtrkngkieeveinTDSAVAQLELYSILqtTWCEQNVSNTISYDPs--- 587 Parachlamydia sp. ...
A6Q367    522 ----------knsYVFAFPIHYDNPRsi----------------kEVDIYEQMLVLTMLqrEWADNMVSNTIQFDPtr-- 573 Nitratiruptor sp. ...
XP_629553 615 ----------stnVVVEIPIHSGKGIrs---------------anSITMWEQLSLASFLqkYWADNQVSCTVSFDPi--- 666 Dictyostelium disc...
NP_682117 600 kllddpfdprcteWLVEIPVAVSWADla---------------gaDTIDVSQFSALAQFdfYMQVQQHYTTHNTSAtiel 664 Thermosynechococcu...
Feature 1                                                                                     
1L1L_A    657 -------EGDQVESLLRQYRfitKSTSLLPYFGGSlq-------qaPKEPIDKETYEKRSQEItgnveevfsql--nsdv 720 Lactobacillus leic...
Q2PDF6    647 ------tEGLHLNQALQYFQyqlKGISFLPRYPMGafk------qmPYEAITKEQYEEAIRKVkedvslssan----aia 710 Euglena gracilis
YP_007110 588 -------EVPAIIDWFMKNWdcyVGVSFLFRNDPTknaedlgyaylPQEVVTKEAYETYCAKLsdidysg---------i 651 Parachlamydia sp. ...
A6Q367    574 ------yDAKDLSQIVKHFLpmiKSLTLLPEKETIyp-------qmPFESIKKEEFEKRVTQLpkvewnt---------l 631 Nitratiruptor sp. ...
XP_629553 667 ------kEGPQLKHALDYFQyqlKGVSFLPNSSTTtsvy----kqmPYEEIDETRYNQIIANLkpvdfqkl-------nn 729 Dictyostelium disc...
NP_682117 665 reaevepLATAIYTAIQQDQg-yISAALLARFDAHetf-----prlPFEPISKERYEQEIAAVarrkrvndfhealsryr 738 Thermosynechococcu...
Feature 1                       
1L1L_A    721 kdlelvDQTDCEGGACPI 738 Lactobacillus leichmannii
Q2PDF6    711 etveenQQTFCDNDRCIK 728 Euglena gracilis
YP_007110 652 hirdddLAEACANGACPI 669 Parachlamydia sp. UWE25
A6Q367    632 sghhadSERFCSTQSCQI 649 Nitratiruptor sp. SB155-2
XP_629553 730 spleptPDKFCDSSSCTI 747 Dictyostelium discoideum
NP_682117 739 qplweaGPAGCDSDQCLM 756 Thermosynechococcus elongatus BP-1

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