4R1R,1PEQ,4R1R,2WGH,1ZYZ


Conserved Protein Domain Family
RNR_I

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cd01679: RNR_I 
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Class I ribonucleotide reductase
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 many viruses, 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, bacteriophages, 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 I RNR is oxygen-dependent and can be subdivided into classes Ia (eukaryotes, prokaryotes, viruses and phages) and Ib (which is found in prokaryotes only). It is a tetrameric enzyme of two alpha and two beta subunits; this model covers the major part of the alpha or large subunit, called R1 in class Ia and R1E in class Ib.
Statistics
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PSSM-Id: 153088
View PSSM: cd01679
Aligned: 52 rows
Threshold Bit Score: 532.504
Threshold Setting Gi: 2914234
Created: 2-Sep-2004
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 15 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                   ##                
4R1R_A    169 AQFLYILVAACLFsnyp----------------------retrLQYVKRFYDAVSTFKISLPTPIMSGVrtp----trQF 222 Escherichia coli
P50620    118 YEDRISIVALFFAng---------------------------dTEKAKEYVNLMINQEYQPSTPTFLNAgrk---rrgEL 167 Bacillus subtilis
NP_051640 118 YEDRLSITALARSe----------------------------rVDEALELVHHLVNQTFTPATPTLMNSgka---ntgRL 166 Deinococcus radiod...
NP_220889  40 FQDLFARVSSHYAe----------------------------nKQHAQKLYEYMSQMWFMPATPILSNGgte----rgLP 87  Rickettsia prowaze...
NP_664853 120 LEDRVLFNALYFAdg---------------------------qEDLAKDLAVEMINQRYQPATPSFLNAgrs---rrgEL 169 Streptococcus pyog...
NP_831135 110 YEDRVAIVSLYLGrg---------------------------dVSKARQFASMIVKQNYQPATPTFLNAgrs---rrgEM 159 Bacillus cereus AT...
NP_950306 188 YEDRLSVNALYHAkg---------------------------dFEIAKRLIVSLINQDFTPATPTLLNTgkk---hrgEF 237 Onion yellows phyt...
YP_006145   8 YEPWYWANAHTRLymrrgyllpgvsveervkeiaqraealtkvEGFGRKFLEYVARGWYSLATPIWANYglr----rgLP 83  Thermus thermophil...
YP_169563  39 PQYAFARAAVAYSfg---------------------------dMNLAHRIYDAAAKGWFMFASPVLSNAplpgvkvksLP 91  Francisella tulare...
AAT68709  109 YEDRIIAVSLFLAdg---------------------------cFEFALKLASEMIKQRYQPATPTFLNAgkr---vrgEL 158 Borrelia hermsii
Feature 1      ##                            #                                                
4R1R_A    223 SSCVLIECG-DSLDSINATSSAIVKYVSQRAGIGINAGRIRALgspirggeafhTGCIPFYKHFQTAVKSASQGgvrgGA 301 Escherichia coli
P50620    168 VSCFLLEVN-DSLNDISRAIDISMQLSKLGGGVSLNLSKLRAKgeaikdvenatKGVVGVMKLLDNAFRYADQMgqrqGS 246 Bacillus subtilis
NP_051640 167 VSCFLLQDCtDNLDSITKTLSFVAELSKGGGGIGVEASNLRARgeslrgiqnvtKGVLGVAKMLDNMLRYADQAgqrpGA 246 Deinococcus radiod...
NP_220889  88 ISCFLNETD-DSLDDIVNLWMENVWLAARGGGIGSYWGNVRSIneair-dkghsSGIIPFIKVMDSMTLAISQGsirrGS 165 Rickettsia prowaze...
NP_664853 170 VSCFLIQVT-DDMNSIGRSINSALQLSRIGGGVGITLSNLREAgapikgyagaaSGVVPVMKLFEDSFSYSNQLgqrqGA 248 Streptococcus pyog...
NP_831135 160 VSCFLLEMD-DSLNSIGFNINTAMQLSKIGGGVALNLSKLRARgeqikgidnaaSGVVPVMKLLEDSFSYANQLgqrkGA 238 Bacillus cereus AT...
NP_950306 238 VSCFLLEAG-DSLNDIARINEFSMQLSKIGGGVSINITNLRAKgesikgikgvcKGVVGVCKLLDHSFRYADQIglrtGA 316 Onion yellows phyt...
YP_006145  84 ISCYGTYVE-DDTASILRAVAEVGMMSKQGGGTSLYLGRLRPRgapir-dngesNGSFAFASLFDRVIEVFNQGstrrGQ 161 Thermus thermophil...
YP_169563  92 ISCFLSYVP-DSLEGLIEHSSELRWLSVKGGGVGGHWSSVRAVsd-------kaPGPIPFMHTVDADMVAYRQGktrkGS 163 Francisella tulare...
AAT68709  159 VSCFLLEVG-DSLNSITFNISSAMQLSKIGGGVALNLSNIRARgeeirgicniaKGIIPVMKLLEDGFNYADQMgqrkGA 237 Borrelia hermsii
Feature 1                                                                                     
4R1R_A    302 ATLFYPMWHLEVESLLVLKNNRGvegn-rvrHMDYGVQINKLMYTRLLkgeditlfspsdvpglydaffadq-eeferly 379 Escherichia coli
P50620    247 GAAYLNIFHRDINDFLDTKKISAdedv-rvkTLSIGVVIPDKFVELARedkaayvfyphtiykeygqhmde--mdmnemy 323 Bacillus subtilis
NP_051640 247 GAVYLSVMHADFSDLLNAKKIATdeda-rlkTLSIGATIPDIFMEKVRcgediyqfyphsffqetgrefts--idwtkey 323 Deinococcus radiod...
NP_220889 166 SAVYLPINHPEIEEFIDIRRPTGgdvnrkslNIHHGITITDEFMQAVEnnmdfdlvspa--------------------- 224 Rickettsia prowaze...
NP_664853 249 GVVYLNVFHPDIIAFLSTKKENAdekv-rvkTLSLGITVPDKFYELARknedmylfspynvekeygipfny--lditnmy 325 Streptococcus pyog...
NP_831135 239 GAVYLNIFHWDIIEFLDTKKINAdeks-riqSLSIGIIVPSKFFELAEknepfhvfapytvykeygkhlddididemyde 317 Bacillus cereus AT...
NP_950306 317 GAVYLNVFHSDIIDFLSTKKLSAdedv-rvkTLSLGVVVPNKMIELARnnevmytffphtvfleygknfadiavdmdywy 395 Onion yellows phyt...
YP_006145 162 CAAYLDVEHPDLEEWLSIQREHSpv-----qSLFWGVSVGDRWLEEMIagd----------------------------- 207 Thermus thermophil...
YP_169563 164 YAAYMDISHPDIIEFLGIRVPTGdvnr-kclNLHHAVNLTDDFMQAVAndqdwklidpd--------------------- 221 Francisella tulare...
AAT68709  238 GAVYLNIFHYDIEDFLDTKKINAdeks-rvqTLSLGVIIPDKFFEIAKqgqsyyafapyslykatgrfmne--idfdley 314 Borrelia hermsii
Feature 1                                                                # # #                
4R1R_A    380 tkyekddsirkqrvkaVELFSLMMQERASTGRIYIQNVDHCNTHspfd--paiAPVRQSNLCLEIALptkplnd------ 451 Escherichia coli
P50620    324 dkfvdnprvkkekinpRKLLEKLAMLRSESGYPYIMFQDNVNKVhan---nhiSKVKFSNLCSEVLQasqvssytd--yd 398 Bacillus subtilis
NP_051640 324 qaladnpnirkkrvsaRRLLEDIAVTQGESGYPYLLFEGNANRAnpi---pnvGTIKMSNLCSEILQpttpsyfhpygqe 400 Deinococcus radiod...
NP_220889 225 ------tkkvankvraRDLWIKLLTTRIETGEPYLLFIDSVNKTipehhkklgLQVKMSNLCSEITLptgidh------- 291 Rickettsia prowaze...
NP_664853 326 delvanpkitktkikaRDLETEISKLQQESGYPYIINIDTANKAnp-----idGKIIMSNLCSEILQvqtpslind--aq 398 Streptococcus pyog...
NP_831135 318 lmsnpkvkkkpldisaRDMLIKIAMIQLESGYPYLMFKSNANNQhpl---kdiGTVKMSNLCTEIFQlqetseind--yg 392 Bacillus cereus AT...
NP_950306 396 dilvanpkvqkkainpRQLLELIAHMQGESGYPYLMFCDNTNQAnt-----sdLKVKFSNLCTEILQptitshykdyhqt 470 Onion yellows phyt...
YP_006145 208 -------------gekRARWAKMLKSRAEVGIPYLFFRDNANQKapevfralgKTIWASNLCTEIMLpss---------- 264 Thermus thermophil...
YP_169563 222 ------dktvrdvikaRKIWETILETRYRTGEPYLNFIDTANRAlpksqkdlgLTIKGSNLCNEIHLvtd---------- 285 Francisella tulare...
AAT68709  315 dllasnpnilkkeikaRDMLVRIARLQFESGYPYIMYQTACNLNnpl---kgiGKIKMSNLCTEIFQiqtpsiigd--yg 389 Borrelia hermsii
Feature 1                 #                                                                   
4R1R_A    452 vndengeIALCTLSAFNLGAInnldELEELAILAVRALDALLDyqdypipa------akrgamgrRTLGIGVINFAYYLA 525 Escherichia coli
P50620    399 eedeiglDISCNLGSLNILNVmehkSIEKTVKLATDSLTHVSEttdirnapa-----vrrankamKSIGLGAMNLHGYLA 473 Bacillus subtilis
NP_051640 401 hrdriglDVSCNLASLVIEQTmhggDLGRVVGAAIRMLDNVARstsvhevpa-----vkrandemRSIGLGAMGLHSFLA 475 Deinococcus radiod...
NP_220889 292 --lgnsrTAVCCLASLNLEYYevwkDDKEFIHSIMLFLDNVLEdfinkapntm--arakyaafreRSVGLGVIGFHSFLQ 367 Rickettsia prowaze...
NP_664853 399 efvemgtDISCNLGSTNILNMmtspDFGRSIKTMTRALTFVTDsssieavpt-----ikhgnsqaHTFGLGAMGLHSYLA 473 Streptococcus pyog...
NP_831135 393 tddiirrDINCNLGSLNIVNVmenkEIREAVHAGMEALTAVSDmtiipnapt-----vkkandelHSVGLGAMNLHGYLA 467 Bacillus cereus AT...
NP_950306 471 qqdeigmDVSCNLASGHMGNMitnnTIQETVFMAMEVMNCVSEntnisyvpa-----vakanfinRSVGFGIMGHHGFLA 545 Onion yellows phyt...
YP_006145 265 ----eeeSFVCCLSSLNLLHYee-wKDTDAVETLVIFLDSVLDdfiekaegipymeravrfakryRAIGLGVLGWHSYLQ 339 Thermus thermophil...
YP_169563 286 ----ekrTAVCCLSSVNLERYde-wKDTSLIKDLIRFLDNVLQffidhagdei--skarysasreRSLGLGAMGFHSYLQ 358 Francisella tulare...
AAT68709  390 egdligyDVSCILGSLNIVNVvn-sNFEYTVDIAMQALTSVCDktdiknaps-----iskanndyHAVGLGVMNLHGFLI 463 Borrelia hermsii
Feature 1                                                                                     
4R1R_A    526 KHGkrysdgsaNNLTHKTFEAIQYYLLKASNELAKEQGacpwfnettyakgilpidtykkd-----------ldtianep 594 Escherichia coli
P50620    474 QNGiayespeaRDFANTFFMMVNFYSIQRSAEIAKEKGetfdqyegstyatgeyfdkyvstdfspkyekianlfegmhip 553 Bacillus subtilis
NP_051640 476 GKEliygspeaLEFVDVFFAAVHYHARKASMEIARDTGfvfsgfegsryqsgehfaqylerdfaprrpevaalfeghtlp 555 Deinococcus radiod...
NP_220889 368 MKKipiesvmaKVWNKKIFEYISAEVDKASIEIGKDKGacpda------------------------------------- 410 Rickettsia prowaze...
NP_664853 474 QHHieygspesIEFTDIYFMLLNYWTLVESNNIARERQttfvgfenskyangsyfdkyvtghfvpksdlvkslfkdhfip 553 Streptococcus pyog...
NP_831135 468 KNKiayesaeaKEFARTFFMMLNYYSIEKSMEIATEKGetfkdfdksdyangtyfekyettdyspvtekvqqlfegihip 547 Bacillus cereus AT...
NP_950306 546 QNYiafgseenKDLIDVFFNAVNFYSLLHSCNKAKTTGkkfyrfeqskyadgsyfdnrgeilpkta--kikkmfqnitlp 623 Onion yellows phyt...
YP_006145 340 SQRiplespeaFRRNAEIFKTIRERAEEASRWLRKRHPedelag------------------------------------ 383 Thermus thermophil...
YP_169563 359 LHRvpfesqraKEINEEIFKRIKEQALEETLILGAEKGeapd-------------------------------------- 400 Francisella tulare...
AAT68709  464 KNKipyesaeaIDFVRTFFMLLNFYSIKSSMNIAKTRGktfkdfkqseyyngnyfnmyltedfspktevvkgifsgikip 543 Borrelia hermsii
Feature 1                              ######                                                 
4R1R_A    595 lhydwealresikthGLRNSTLSALMPSETSSQISN-ATNGIEPPRg-yVSIKASk-dGILRQVVPDYehlhday----- 666 Escherichia coli
P50620    554 ttedwkklkafvaehGMYHSYRLCIAPTGSISYVQS-STASVMPIMe-rIEERTYg-nSKTYYPMPGLasnnwff----- 625 Bacillus subtilis
NP_051640 556 tradweqlvedikthGLAHSFVMAIAPTGSISYVSH-ASASIMPITe-kVETRTSn-kARTIYPMPHLsedtewy----- 627 Deinococcus radiod...
NP_220889 411 ----------ldsgsNERFSNKTAIAPTASISVIAGnASPGIEPFAa-nSFVQKTl-tGSFNVRNKHLeqlleekgfnnd 478 Rickettsia prowaze...
NP_664853 554 qasdwealrdavqkdGLYHQNRLAVAPNGSISYIND-CSASIHPITq-rIEERQEkkiGKIYYPANGLstdtipy----- 626 Streptococcus pyog...
NP_831135 548 tkedwtslkeqvqknGLYNSYRLAIAPTQSISYVQN-ATSSVMPIVs-qIESRTYa-nATTYYPMPYLskdtfwy----- 619 Bacillus cereus AT...
NP_950306 624 tqkdwhqlkqdvmqfGLYNSHRLAVAPNGSIGYIMG-ATPSLTPVKq-lVEERTYg-nSKTYCPMPALkqtsfmy----- 695 Onion yellows phyt...
YP_006145 384 ----------vgelkERRNATLLAIAPTKSSAFILGqVSPSIEPYTs-nYYLKDLq-kARVPFKNPFLeevlrekgkdee 451 Thermus thermophil...
YP_169563 401 -----------magtGRRNAHLLAIAPNANSSLILN-TSPSIEPWKanaFTSRTRv--GSHLNKNKYLeqelekigknte 466 Francisella tulare...
AAT68709  544 lksdwenlkrdvqmhGLYHAYRLAVAPTQSISYIQN-ATTSLMPIVe-pVEARVYg-nSTTYYPMPYLskenalf----- 615 Borrelia hermsii
Feature 1                                                                                     
4R1R_A    667 --------------------------ellwempGNDGYLQLVGIMQKFIDQSISANTNYDPsrfp-------sgkvPMQQ 713 Escherichia coli
P50620    626 --------------------------ykeaydmDMFKVVDMIATIQQHIDQGISFTLFLKDt-------------mTTRD 666 Bacillus subtilis
NP_051640 628 --------------------------yeeaydmDQRRVLDTVAAAQKHVDQGISCTLFLPAs-------------aTTRT 668 Deinococcus radiod...
NP_220889 479 qvwssiathegsvqhltflseeekqifktayeiDQNWLIELAADRTPYITQSQALNIFLHGn-------------vSKKY 545 Rickettsia prowaze...
NP_664853 627 --------------------------ytsaydmDMRKVIDVYAAATEHVDQGLSLTLFLRSelpmelyewktqskqTTRD 680 Streptococcus pyog...
NP_831135 620 --------------------------ykssydmNQFKLIDLIAEIQEHIDQGISTILYVNSd-------------iSTRE 660 Bacillus cereus AT...
NP_950306 696 ---------------------------ttaykmNKYDLIDVIAIAQKHVDQGISFELGITSd-------------iTTRE 735 Onion yellows phyt...
YP_006145 452 kvwrsilehngsvqhldfltdeekavfktfaeiSQMTLVNLAASRQKHIDQGQSLNLVIHPe-------------aPPRD 518 Thermus thermophil...
YP_169563 467 evwsdiitnggsvqqldflskelkevfktaiemDQDWLVYLGGERQKYLCQGQSLNVFFPAg-------------aSRGY 533 Francisella tulare...
AAT68709  616 --------------------------fksayymDMRKLIDLISEAQRHVDQGISTLLYVTNe-------------tSTRE 656 Borrelia hermsii
Feature 1                          
4R1R_A    714 LLKDLLTAYKFGVKTLYYQNT 734 Escherichia coli
P50620    667 LNRIDLYAHHRGIKTIYYART 687 Bacillus subtilis
NP_051640 669 LQSYYLYAYRLGIKTLYYTRL 689 Deinococcus radiodurans R1
NP_220889 546 LNNIHFKAWKKGIKSLYYCRS 566 Rickettsia prowazekii str. Madrid E
NP_664853 681 LSILRNYAFNKGIKSIYYIRT 701 Streptococcus pyogenes MGAS315
NP_831135 661 LARYYIYAHKKGLKSLYYTRT 681 Bacillus cereus ATCC 14579
NP_950306 736 LQKYYLYAHHKKIKTLYYTRT 756 Onion yellows phytoplasma OY-M
YP_006145 519 VNALVLHAWRSGLKALYYQFS 539 Thermus thermophilus HB27
YP_169563 534 LHKVHFNAWKYGCKGLYYLRT 554 Francisella tularensis subsp. tularensis SCHU S4
AAT68709  657 LVKLYIYAKNKGLKSLYYTRN 677 Borrelia hermsii

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