1KGN,1AV8,1JK0,1JK0,1KGO,2UW2,2VUX,1UZR,2R2F,2O1Z,2P1I,2ANI,1SYY,2RCC,2ALX,1PM2


Conserved Protein Domain Family
RNRR2

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cd01049: RNRR2 
Click on image for an interactive view with Cn3D
Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain
Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-helical bundle; some have 2 addition beta strands. Yeast is unique in that it assembles both homodimers and heterodimers of RNRR2. The yeast heterodimer, Y2Y4, contains R2 (Y2) and a R2 homolog (Y4) that lacks the diiron center and is proposed to only assist in cofactor assembly, and perhaps stabilize R1 (Y1) in its active conformation.
Statistics
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PSSM-Id: 153108
View PSSM: cd01049
Aligned: 156 rows
Threshold Bit Score: 129.282
Threshold Setting Gi: 184156149
Created: 24-Sep-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 6 residues -Click on image for an interactive view with Cn3D
Feature 1:diiron center [ion binding site]
Evidence:
  • Structure:1KGO; Corynebacterium ammoniagenes Ribonucleotide reductase R2 subunit diiron center: reduced
    View structure with Cn3D
  • Structure:1KGN; Corynebacterium ammoniagenes Ribonucleotide reductase R2 subunit diiron center: oxidized
    View structure with Cn3D
  • Comment:In the oxidized state, the irons are symetrically bridged by a mu-oxo-bridge.
  • Comment:The active form of the metal cofactor carriers the ferric [Fe(III)Fe(III)] state together with the tyrosyl radical.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                  #                     
1KGN_A        19 INWNVipDEKDLEVWDRLTGnFWLPEKIPVSNDIQSWNkmtPQEQLATMRVFTGLTLLDTI-----QGTVGAISLLPda- 92  Corynebacterium...
1KGO_A        19 INWNVipDEKDLEVWDRLTGnFWLPEKIPVSNDIQSWNkmtPQEQLATMRVFTGLTLLDTI-----QGTVGAISLLPda- 92  Corynebacterium...
P28847        21 FFYTPe-CPDIEHLRSLSVAnRWLDTDLPISDDLKDVAkltPAEREFYRFLFAFLSAADDL-----VNLNLGDLSALft- 93  Equine herpesvi...
AAD56212       9 YYYLPq-CDDIRELRDLSIAnNWNEFELCYSRDEKDVDlltPEELDFYKLVFAFLAAADDL-----INLDIGNLMTLfl- 81  ILTV
NP_065559      7 YLYVCd-HPGFFELTQETFQnRWFPAQINLSVDVKCLSlmsEADVNFYKYLFTFLGMAETL-----VNFNIDELLVDfe- 79  wildebeest herp...
EAA19522      29 WVMFPikYKTFWNYYKEIESlFWTAEDHNFDKDKPFLNsmdKTTLSKLLELFCFYSLKDLHl----RDEQAIITSKLldi 104 Plasmodium yoel...
YP_002730338  17 RLTENprYPVFKEIYTKQKKaVWFPEELNIQQDVLDYKsltPTEKDLFDTSVGYFASSELL-----VQNVLGNGFFPvl- 90  Persephonella m...
XP_001610573  31 WVMFPihYDALWAMYKEIENsFWAAEDFRFANERDTYSslpTELRQLVVKLISYHNRLDRSevarpATITLDLLADTq-- 108 Babesia bovis T2Bo
XP_766717     32 WVMFPieHDTFWIMYKEVENnFWAAEDFIFSDDLNSLFklpKPLFNSLFHLLSFHINLDNKwv-crPVDMTLELLSEvq- 109 Theileria parva...
XP_953574     28 WVMFPieHDTFWILYKEVENnFWAAEDFIFTDDIKLLYqlpKPIFNTLLNLLSFHINLDNKlicrpVDITLDLLSEVq-- 105 Theileria annul...
Feature 1                        #  #                                                            
1KGN_A        93 -etMHEEAVYTNIAFMESVHAKSYSNIFMTLastp--qineAFRWSEENENLQRKAKIIMSYYNGd-------------- 155 Corynebacterium...
1KGO_A        93 -etMHEEAVYTNIAFMESVHAKSYSNIFMTLastp--qineAFRWSEENENLQRKAKIIMSYYNGd-------------- 155 Corynebacterium...
P28847        94 --qKDILHYYIEQESIEVTHSRVYSAIQLMLfgndaaararYVASIIGDAAIGRKVAWLQAKVREcg------------- 158 Equine herpesvi...
AAD56212      82 --hKDIQHYYAEQIRIETVHSRTYSLVQMILfkgdlhardrYVTEAIKDPAIKKKIDWLNRVQVEtd------------l 147 ILTV
NP_065559     80 --cHDIKHYYCEQMAMECVHGKVYFNILNMLfknnlaatweFAEAVLKDEALQKKLEWLESKIKMak------------- 144 wildebeest herp...
EAA19522     105 iqiPEGRAFYGFQMCMENIHNEVYACIFESYsldsk-qkkeIIDKVLKYESVFKKQNWLYNEFEAni------------- 170 Plasmodium yoel...
YP_002730338  91 -tdPYAKMSFSTQMFMENIHSDFFEIILNTFemd----rkrIYNITLEDKLLMEKQELIIRAVDRitygkadpdtlegkk 165 Persephonella m...
XP_001610573 109 --iPEARAFYGFQVSYENIHSELFGIMSSAIp---------GTIDVPEADAKIEWLTRNLTSTSC--------------- 162 Babesia bovis T2Bo
XP_766717    110 --iAEARAFYGFQLTDENIHTETIGTMFQLL----------NQPLDNTIGQDKITWLYNECEKNKc-------------- 163 Theileria parva...
XP_953574    106 --iAEARAFYGFQLTDENIHTETISSMFQLFnqq----ldtNIVSSNTLFLSSYGMDKIIWLYNEcen----------nk 169 Theileria annul...
Feature 1                     #                                  #  #                            
1KGN_A       156 dPLKKKVAs-TLLESFLFYSGFYLPMYLSSRA-KLTNTADIIRLIIRDESVHGYYIGYKYQQGvkklse-aeqeeyKAYT 232 Corynebacterium...
1KGO_A       156 dPLKKKVAs-TLLESFLFYSGFYLPMYLSSRA-KLTNTADIIRLIIRDESVHGYYIGYKYQQGvkklse-aeqeeyKAYT 232 Corynebacterium...
P28847       159 sVAEKYILm-ILIEGLFFASSFASIAYLRTHN-LFVVTCQSNDLISRDEAIHTRASCCIYNNYlggf-----ekpePKRI 231 Equine herpesvi...
AAD56212     148 tLPEKYILm-ILLEGIFFVASFAAIAFLRRRN-IFVVMCQSNDLISRDEAVHTTASCRIYNNWlgdh-----kkpsAKRI 220 ILTV
NP_065559    145 tKAEKVLIf-YLIEGVFFISSFYCIGLLRVKG-VMPGVCMANDYISRDELLHTRAAALLYNTMipke-----erpsSEWV 217 wildebeest herp...
EAA19522     171 pFYNKLIL--LYISKVLFNGGFSILASYCKENnILSSFTGVHAKIQRDEYLQGDFSVMCCNHLnnk--------lrYENV 240 Plasmodium yoel...
YP_002730338 166 qILTAILLnnIIQEGMFFYSAFAHFFAMKDTG-KMKNVVSGVELILIDESLHLQNGIEAILTIveenpeivddekfVENI 244 Persephonella m...
XP_001610573 163 -FYIKVIL--QCISKAIFRSAFGILADYLRNSkKLPTLLSALDTVAKDVSIHLKFAMAALEHLklr--------ptRETV 231 Babesia bovis T2Bo
XP_766717    164 -FFKRVLL--VVISKLLFTATFNILRDYLVKEkLLPTFTLALDAVSKDRHIHTRFAHCTFTLLqhk--------mlESDV 232 Theileria parva...
XP_953574    170 cFFKRVLL--LVIMKLLFYCSINILRDYLLKEkLLPTFITAFDSITNDRIIHTRFAHCTFRLLqnk--------mlESEV 239 Theileria annul...
Feature 1                                                                                    
1KGN_A       233 FDLMYDLYENEIEYTEDIYd------dLGWTEDVKRFLRYNANKALNNLGYEGLFptde---tkvsPAILSSLSPN 299 Corynebacterium amm...
1KGO_A       233 FDLMYDLYENEIEYTEDIYd------dLGWTEDVKRFLRYNANKALNNLGYEGLFptde---tkvsPAILSSLSPN 299 Corynebacterium amm...
P28847       232 YELFSEAVNIECEFLLSHApqy---shLLDIGAIISYVRYSADRLLGEIGLSPLFnap-----kpsPSFPLAFMTV 299 Equine herpesvirus ...
AAD56212     221 HQLFKEAIEIECNFLASRApqa---srLIDLEAIQSFVRYSGDRLLTAIGVPTIFdep-----ppdPSFPLTLMSI 288 ILTV
NP_065559    218 VSLFKEAVEIECAFIEAKTkq----vtFVSMDDIRAFLEATADRLLNSIELPRYYks-------dpPQSCPLTYTG 282 wildebeest herpesvirus
EAA19522     241 LNYFKAAVELEYNFCVDMLdfd---flKITKDQVKQFLQYLADTMLLNLKYPKHYns-------kyPFAWKEFSKV 306 Plasmodium yoelii y...
YP_002730338 245 KETIIDAVELELNYLKTKFggt--tifGVSYKELEKYMKYIADRRLEELGFDPQFkid------qnPLKFLQKEDV 312 Persephonella marin...
XP_001610573 232 MELLNSAYDLEMAYCRSVLpmd---hmGLSEYHLSQYIKNNVNQCLLITGNTEEHrvkve-lgwlkPSIFTGNAST 303 Babesia bovis T2Bo
XP_766717    233 VQLIKEALKLEYDFANKFLplslmaitQMLTDVLRGYMEWVGNNVLMVCGYRTLY-----------SSDFDVEWLN 297 Theileria parva str...
XP_953574    240 LEIIKQALKLEYQFILQYFtiq---ffNLSTNVIKSYLEWIGNNILLVCGYKTLYtsefdidwlnhPIIDLNIQKQ 312 Theileria annulata ...

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