1HK8


Conserved Protein Domain Family
RNR_III

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cd01675: RNR_III 
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Class III 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 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 strict or facultative 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). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit which contains the active and allosteric sites.
Statistics
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PSSM-Id: 153084
View PSSM: cd01675
Aligned: 28 rows
Threshold Bit Score: 532.642
Threshold Setting Gi: 26553948
Created: 7-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 8 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                                                                             #         
1HK8_A       21 ENANKDs-----rVFPTQRDLMAGIVSKHIAKNm-------VPSFIMKAHESGIIHVHDIDYspalpFTNCCLVDLKGML 88  T4
NP_623435   122 ENSNMSy-----sLQGLNNHISSSITAHYWLNKi-------YPPEVRDAHISGDLHIHDLGLl----SVYCCGWDLRDLL 185 Thermoanaerobact...
CAE48969     25 ANANQDy-----sLGGMILNAAGKVTANYWLDQv-------FSPAASAAHREGSIHIHDLDMl----SGYCAGWSLRQLL 88  Corynebacterium ...
YP_009523   118 ENANMTh-----sFQGLMLHLSGTLQAKYALDK--------YPEEVRQAHEHGYFHIHDLSFg---lAGYCAGWSLRDLL 181 Desulfovibrio vu...
NP_522524   119 ANANQGy-----sLGGLILNVAGKVTANYWLSHv-------YSPEAGHAHREGDLHIHDLDMl----SGYCAGWSLRQLL 182 Ralstonia solana...
NP_250610   126 ANANQGy-----sLGGLILNVSGKVTANYWLDEv-------YDADIAAAHRDADLHIHDLDMl----AGYCAGWSLRTLL 189 Pseudomonas aeru...
NP_971937   153 ENANVNf-----sLGGLILHNSGTITANYWLKNi-------YTPAIAEAHITAAFHIHDLSMf----SGYCAGWSLRQLI 216 Treponema dentic...
NP_963632    33 ENANQY-------PGPTGFFAYVLEKAMEEHLTi-------MPERPLKAHLNKDIYIHKLPLal--yVPYCSGHSLARVL 96  Nanoarchaeum equ...
ZP_00134686  33 ANANVTqkniatmENEMMKDFFVQINRAKVSNKiaelfdeeLAGEYLRQIESHEIYVHDETSl----KPYCVSVTMYPFL 108 Actinobacillus p...
YP_154580    33 ANANVTqkniatlEAELMKDFFVQVNRKQVSNKiselfgneLAKEYVRQIEDHEIYVHDETSl----KPYCVSVTMYPFL 108 Idiomarina loihi...
Feature 1                                              #                                        
1HK8_A       89 ENGFKLGNAQIE--TPKSIGVATAIMAQITAQVASHQYGGTTFANVDKVLSPYVKRTYAKhiedaekwqiadalnyaqsk 166 T4
NP_623435   186 LNGFTGVEGKVQskPPKHFRSALGQIVNFFYTLQGEAAGAQAFSNFDTYLAPFVYYDNLSyr------------------ 247 Thermoanaerobact...
CAE48969     89 EEGFGGVPGTISsrPPKHFSSACGQIVNFLGTLQNEWAGAQAFSSFDTYMAPFVRLDNLSyd------------------ 150 Corynebacterium ...
YP_009523   182 LEGFNLENRSSAg-PAKHLDTALGQMINFLGTLQNEWAGAQAFNNVDTYLAPFVRNDGLTyk------------------ 242 Desulfovibrio vu...
NP_522524   183 TEGFNGVPGKVEatPPRHMSAAIGQIVNFLGTLQNEWAGAQAFSSFDTYMAPFVRRDAMSya------------------ 244 Ralstonia solana...
NP_250610   190 NEGLNGVPGRVEagPPKHLGSALGQMVNFLGTLQNEWAGAQAFSSFDTYLAPYVRKDRLDya------------------ 251 Pseudomonas aeru...
NP_971937   217 HEGLGGVPDKITskPPKHLSTLIQQIVNFLGIMQNEWAGAQAFSSFDTYLAPFVKKDKMSea------------------ 278 Treponema dentic...
NP_963632    97 EKGMITPTVISK--PAKHFDTFVDHVANFLIIAQQHFTGAQAFSSVEWYAGPFIRNDRLDyk------------------ 156 Nanoarchaeum equ...
ZP_00134686 109 HDGLTKLGGESK--APKHLASFCGSFVNFVFAVSSQFAGAVATVEFLTYFDYFARKDFGDnyltt--------------- 171 Actinobacillus p...
YP_154580   109 RDGLTKLGGESQ--APKHLESFCGTFVNFVFAVSSQFAGAVATVEFLTYFDYFARKDYGDdylnt--------------- 171 Idiomarina loihi...
Feature 1                                   #                                                   
1HK8_A      167 tekdvYDAFQAYEYEVNT-LFSSNGQTPFVTITFG-----------------------TGTDWTERMIQKAILKNRIKGl 222 T4
NP_623435   248 ---evKQAMQEFIFNLNV-PTRVGFQTPFTNITMDlvvpeimadepviiggkimdrtyKEFQKEMDMINMAFAVVMMEGd 323 Thermoanaerobact...
CAE48969    151 ---eiVQDMQEFIFNLNV-PSRWGTQTPFTNLTFDwtcpadlkdsvpfigeepvdftyGELQEEMDLINRAFIQVMSAGd 226 Corynebacterium ...
YP_009523   243 ---qvRQAMQKFVFNLNT-TSRWGGQSPFTNLSFDlvppkhianepviiggayqdatyGDYAPEMEMLNRAFIEVMLDGd 318 Desulfovibrio vu...
NP_522524   245 ---avKQAMQELIYNLNV-PSRWGTQTPFTNLTFDwtcpadlreqipylggeempftyGDLQPEMDMINRAYIEVMMAGd 320 Ralstonia solana...
NP_250610   252 ---svRQALQEFIYNLNV-PSRWGTQTPFTNLTFDwvcpddlrdqvpriggeempfayGELQAEMDLINRAYIEVMQAGd 327 Pseudomonas aeru...
NP_971937   279 ---nvKQCLQSFVYGVNT-PSRWGSQAPFTNITLDwvcppdlanqkavvggetqdftyGDCQKEMDMINKLFIELMLEGd 354 Treponema dentic...
NP_963632   157 ---qiKQNIQRMVFNLNY-PSRIGMQSPFTNFTVTmdaatsilegdyayydgkkvaplGEYEKEAKLFLLALTEVLREGd 232 Nanoarchaeum equ...
ZP_00134686 172 hrseiENHLQQVVYSINQpAAARGYQSVFWNISLYdkhyfeamf-----gnfvfpdfeRPNWETTAALQIFFMKWFNQEr 246 Actinobacillus p...
YP_154580   172 hrhqiENHLQHVVYALNQpAAARGYQSVFWNISIYdqhyfdsmfg----efvfpadftKPEWNSVSALQDFFLDWFNKEr 247 Idiomarina loihi...
Feature 1                                                                         ##            
1HK8_A      223 grdGITPIFPKLVMFVEEGvnlykddpNYDIKQLALECASKRMYPDIISAKNNKAItgssvpvsPMGCRSFLsvwk---- 298 T4
NP_623435   324 a-kGRIFTFPIPTYNITKNfd-----wDSPVVNKVMEMTAKYGLPYFSNFVNSDLDpnd---vrSMCCRLRLdnrelr-- 392 Thermoanaerobact...
CAE48969    227 a-dGRPFTFPIPTYNITKDfd-----wDSPNTEALFTMTAKYGLPYFQNFINSDLDpgm---irSMCCRLQLdlrell-- 295 Corynebacterium ...
YP_009523   319 h-nGRIFSFPIPTYNVTTDfp-----wESEIGDLLLKLTARYGVPYFQNFINSDLNped---vrSMCCRLQMdlrelr-- 387 Desulfovibrio vu...
NP_522524   321 a-kGRAFTFPIPTYNITPDfd-----wDHPNTKRLFEMTARYGLPYFQNFLNSDLEphm---vrSMCCRLQLdlrell-- 389 Ralstonia solana...
NP_250610   328 a-hGRVFTFPIPTYNITHDfp-----wDSDNATRLFEMTARYGLPYFQNFLNSDMQpnq---vrSMCCRLQLdvrell-- 396 Pseudomonas aeru...
NP_971937   355 a-aGRGFQYPIPTYNITSDfd-----wSSPNAKLLFEMTARYGTPYFQNFINSDLNpgd---vrSMCCRLQLdkrelr-- 423 Treponema dentic...
NP_963632   233 a-iGQPFTYPIPTLMASAPml----wnDPEIYEAIFKTAAKRGSFYWLNTNVVDPNas-----fAMCCRINIdknelkfa 302 Nanoarchaeum equ...
ZP_00134686 247 --sKAILTFPVVTAAMLTEn------gKCKDNEFADQMAEELSQGNSFFIYQSDNPds-----lASCCRLRNeisdht-- 311 Actinobacillus p...
YP_154580   248 --eKTILTFPVVTVAMLTNe------gECKDQLFAEKIAGEMANGNSFFVYLSDNAds-----lASCCRLRSeisdnt-- 312 Idiomarina loihi...
Feature 1                                        #                                              
1HK8_A      299 -------------------dstgNEILDGRNNLGVVTLNLPRIALdsyigtqfnEQKFVELFNERMDLCFEALMCRISsl 359 T4
NP_623435   393 -----------------rrggglFGANPLTGSIGVVTINMPRIGYls-----rtKEEFFQRLERLMDIAKTSLEIKREvl 450 Thermoanaerobact...
CAE48969    296 -----------------krgnglFGSAELTGSIGVVTLNCARLGYlya----gdEQALLGAVDELIELGIDTLERRRDfv 354 Corynebacterium ...
YP_009523   388 -----------------nkvgglFGAGDLTGSIGVVTLNLPKLAYla-----qgEEDFLDLVAEYAEIAKDSLEFKRKli 445 Desulfovibrio vu...
NP_522524   390 -----------------krgnglFGSAEQTGSIGVVTVNCARLGHlha----gdEAALMARLDTLLALGRDVLEVKRKfv 448 Ralstonia solana...
NP_250610   397 -----------------krgnglFGSAEQTGSLGVVTINCARLGYrhr----gdAAGLYRQLDHLLELAFASLELKRKvi 455 Pseudomonas aeru...
NP_971937   424 -----------------krggglFGSDEFTGSIGVVTINMPQIGYls-----ktEKDYFDRLDYLMDIAKQSLEIKRKvi 481 Treponema dentic...
NP_963632   303 fsvkkkdederikeiekqrfgglWAMPDVTGSIQVTTINLPRLALea-----kdDDKFWELYAEKLTIIKEIEDWFREry 377 Nanoarchaeum equ...
ZP_00134686 312 ------------------fsyslGAGGVATGSINVITINMNRLVQdg-----rdLEEEVGKIHKYQYAYRKLMEEYLA-- 366 Actinobacillus p...
YP_154580   313 ------------------fsytlGAGGVATGSINVITMNMNRLVQdg-----rdLEEEVSKIHKYQVAYRKLMEEYKK-- 367 Idiomarina loihi...
Feature 1                                                                                       
1HK8_A      360 kgvkaTVAPILYQEGafgvrlkpdddiielfkngrSSVSLGYIGIHELNILVG-----------------RDIGREILTK 422 T4
NP_623435   451 ekmteMGLYPYSKFYlrdvkkr------fgyywqnHFNTIGLIGMNEALLNFMgvsia--------teegRKFALEVLDF 516 Thermoanaerobact...
CAE48969    355 athmrQGLYPYSARWlps--------------ldnHFSTIGVNGCNEMIRNFThdaynl------tdpqgHAQVARLLDH 414 Corynebacterium ...
YP_009523   446 tenldRGMFPWSRRYlkng-------------frgHFSTIGLVGGHEACMNLLgkgid--------seagVRLMQRTLNH 504 Desulfovibrio vu...
NP_522524   449 qrlidQGLYPYTRRYlgt--------------lrnHFSTLGVNGVNEMIRNFSgdaddi------ttpagHAMAVRLLDH 508 Ralstonia solana...
NP_250610   456 qqhmdAGLYPYTRRYlgt--------------lrnHFSTIGVNGLHEMVRNFSddregl------hseagREMALALLDH 515 Pseudomonas aeru...
NP_971937   482 eklleGGLFPYTKRYlhh--------------lnnHFSTIGICGMNESCLNFLgediv--------sprgKAFAEKVLTY 539 Treponema dentic...
NP_963632   378 v-kliRTHKEMYKFFhsylw----------dfpssHFNTIGIIGLPEAAAIYMnnpelwfegsrkdwleaAKLMRDMVRF 446 Nanoarchaeum equ...
ZP_00134686 367 -----AGMLPVYDAGfis--------------ldkQFLTIGINGMAEAAESQGltvgy--------nsdyMQFVQSRLKV 419 Actinobacillus p...
YP_154580   368 -----AGLLTVYDAGfit--------------ldkQFLTIGINGMVEAAESQGita------------gnNEAYKDFVQS 416 Idiomarina loihi...
Feature 1                           #  #                                                        
1HK8_A      423 MNAHLKQWTERTGFAFSLYSTPAENLCYRFCKLDTEKYG--SVKDVTDKGWYTNSFHVSVEENITPFEKISREAPYHFIA 500 T4
NP_623435   517 MRHKLEQYQLESSFMYNLEATPAEGASYRLAKKDKELFPd-IITAGDDVPYYTNSTQLPVDFTEDIFTALDLQEELQTKY 595 Thermoanaerobact...
CAE48969    415 INARLVQAQERTGHLFNLEATPAEGTTYRLAKEDLKRYPdmLHAGTPEEPYYTNSSQLPVSHTPDPFEALALQEDLQSKY 494 Corynebacterium ...
YP_009523   505 LREVTTRFQEETGNLYNLEATPAEGTSYRLAKIDKTLYSe-IRASGNGTPYYTNSTALPVGLTEDVFNALEHQNRLQPLY 583 Desulfovibrio vu...
NP_522524   509 VRLRMAEFQEATGHLYNLEATPAEGTTYRFAREDRKRWPdiLQAGTPEQPYYTNSTQLPVGYTDDPFEALARQEALQGKY 588 Ralstonia solana...
NP_250610   516 VRARLVGFQEDSGHLYNLEATPAEGTTYRFAREDRKRYPriLQAGTPEAPYYTNSSQLPVGFTDDPFEALELQDALQCKY 595 Pseudomonas aeru...
NP_971937   540 MRNRLADFQEETGSLFNLEATPAESTSYRLARHDKNQFPd-IISSGDAEPYYTNSSQLPVAYTTDVFEALDHQESLQRKY 618 Treponema dentic...
NP_963632   447 AVKYAREWMKMDGTPWNVEEVPGESAAAKLAIADAKKYPevLNYLNDPENPIYSTSVAPYYGALELSDRIRIESMVQPEF 526 Nanoarchaeum equ...
ZP_00134686 420 IFEANQTASKKYGVKFNTEFVPAENLGVKNAKWDKADGYf-VPRDCYNSYFYVVEDENTNALDKFLLHGKELIEWLDGGS 498 Actinobacillus p...
YP_154580   417 HLKVIYDANKAAKKEYGYMFNTEFVPAENLGVKNAKWDRs-DGYKVSRDCYNSYFYAVEDEDANALDKLVLHGKELIEYL 495 Idiomarina loihi...
Feature 1                                                                                       
1HK8_A      501 TGGHISYVELPDmknNLKGLEAVWDYAAQh-lDYFGVNMPVd-kCFTCGSthemtptenGFVCSICGetdpkkmnTIRRT 578 T4
NP_623435   596 TGGTVFHGFIGEaisDVETCKALVRKIAYnyrIPYYTITPTfsiCEDHGYis-----geHFECPYCGre----ceVYSRV 666 Thermoanaerobact...
CAE48969    495 TGGTVLHLYMGAamsDGKACAALVRRALTnfhLPYITITPTfsiCPDHGYis-----geHPECPQCGat----teMWTRV 565 Corynebacterium ...
YP_009523   584 TGGTVFHTYLGEavaDPAAIRNFIVKAFTrtkIPYLSITPTfsiCKDHGYlq-----geHHQCPSCGqd----aeVYTRI 654 Desulfovibrio vu...
NP_522524   589 TGGTVLHLYMNEaisSPQACKQLVRRALSnfrLPYITITPTfsiCPKHGYls-----ghHAFCPKCDae-----lLAQQA 658 Ralstonia solana...
NP_250610   596 TGGTVLHLYMAErisSAEACKTLVRTALGrfrLPYLTVTPTfsiCPRHGYla-----geHEFCPKCDeell-qrsTPKSC 669 Pseudomonas aeru...
NP_971937   619 TGGTVFHIFLGEsikDWESCRDLVKAVANnyrIPYFSISPTfsiCPVHGYle-----geHFECPYCK--------REKQA 685 Treponema dentic...
NP_963632   527 TGGVMMHIFLGEq-pEPDALAALTKKILKt-kIVYWSFTPAitvCNHCKKsyt----glYTQCPSCGstd---veIWSRI 597 Nanoarchaeum equ...
ZP_00134686 499 ALHLNLDEALTQs--GYRSLLDIAAKTGC---NYFCINVKIt-iCNECSHidk----rtLCSCSKCGsqn---idYGTRV 565 Actinobacillus p...
YP_154580   496 DGGSALHLNLDEk-lNTSGYLSLLNIAAKtgcNYFCINVKIt-iCNACEQidk----rtLSECSSCGsed---idYGTRV 566 Idiomarina loihi...
Feature 1             
1HK8_A      579 CAYLGN 584 T4
NP_623435   667 VGYYRP 672 Thermoanaerobacter tengcongensis MB4
CAE48969    566 MGYFRP 571 Corynebacterium diphtheriae
YP_009523   655 VGYYRP 660 Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough
NP_522524   659 HAGCGC 664 Ralstonia solanacearum GMI1000
NP_250610   670 CGGCGG 675 Pseudomonas aeruginosa PAO1
NP_971937   686 KLELKL 691 Treponema denticola ATCC 35405
NP_963632   598 IGYYRP 603 Nanoarchaeum equitans Kin4-M
ZP_00134686 566 IGYLKR 571 Actinobacillus pleuropneumoniae serovar 1 str. 4074
YP_154580   567 IGYLKR 572 Idiomarina loihiensis L2TR

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