Conserved Protein Domain Family
Radical_SAM

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cd01335: Radical_SAM 
Click on image for an interactive view with Cn3D
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.
Statistics
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PSSM-Id: 100105
View PSSM: cd01335
Aligned: 57 rows
Threshold Bit Score: 40.7798
Threshold Setting Gi: 35213344
Created: 4-Jun-2008
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
FeS/SAM binding
Conserved site includes 16 residues -Click on image for an interactive view with Cn3D
Feature 1:FeS/SAM binding site
Evidence:
  • Structure:1TV8; Staphylococcus aureus MoaA with a bound 4Fe-4S cluster and S-adenosylmethionine (SAM)
    View structure with Cn3D
  • Structure:2A5H; Clostridium lysine-2,3-aminomutase with a bound FeS cluster and S-adenosylmethionine (SAM)
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1               # # # ###                                                           # ## 
2YX0_A        74 MTPvlaWCTHNCIFCWrpmenflgtelpqpwddpafiveesikaqrklligykgnpkvdkkkfeeawnPTHAAIsLSGEP 153
1TV8_A        18 LSVt-dRCNFRCDYCMpkevfgddfvflpknel------------------ltfdemariakvyaelgVKKIRI-TGGEP 77
gi 1653098    54 LEPl-fRCNLACQGCGkiqhpteilkqnl--------------------------spedcfraveecgAPVVSI-PGGEP 105
gi 77920251   29 LELs-rQCDLRCLYCYadsgtaladelals------------------------eiyavleqamalgiRRVVVL-GGGEP 82
gi 19887507   21 VFVt-gVCNRGCWYCPvsprkkgsdvsfaner--------------------pirserdlvkeaelmdAEGASL-TGGDP 78
gi 20094510   97 IDVt-nRCNMNCPVCFanaeakgyvyepsleq---------------------ieemldllrserpvpAPAVQF-AGGEP 153
gi 32363222   14 IELt-hRCPLHCPYCSnplelvrreaeltc------------------------eqwtdiltqarelgVVQMHF-SGGEP 67
gi 84703591   36 LNTg-tLCNIACENCYilsspqnddlvylsr-----------------------dearpyldearemgAREIGI-TGGEP 90
gi 149735274  10 VIVt-yRCNARCSMCNrykapskpeee------------------------------isietikklpkMYFTNI-TGGEP 57
gi 4981355   114 LSPt-yACNLNCVGCYaglygrkyelshd--------------------------evrdilkqandlgIYFFII-TGGEP 165
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                  ###                             #                     
2YX0_A       154 mlyp-ymgDLVEEFhkr---gfTTFIVTNgtipe----rleeMIKEDkl---ptQLYVSITAPdietynsvnipmipdgw 222
1TV8_A        78 lmr--rdlDVLIAKlnqidgieDIGLTTNgll-------lkkHGQKLyda-glrRINVSLDAIddtlfqsin-----nrn 142
gi 1653098   106 llhp-qidEIVRGLvar---rkFIYLCTNail-------lekSLDKFqps-pylTFSVHLDGPrehhdkcvd------rq 167
gi 77920251   83 lmyp-hvvEIMQYLaqh---giGIDLFTNgtqi------taeLAQEFvrl--gvAPVVKMNSRrqqvqdfla-----grq 145
gi 19887507   79 ltrleravNIIRTLkdefgddfHIHLYAPa-----------eSVREGai---eeLDGVGLDELrvhpsp----------- 133
gi 20094510  154 lvre-divEIVAAAder---gfHVQIATNgvefa----rnpeLAEDLhaa-glnVVYLQFDGLnpeiyeeir-----gsr 219
gi 32363222   68 larp-dlpDLVGHArrl---gaYVNLVTSgvgl------taeRAHDLarr-gvdHVQLSLQDAdpaagqaia------ga 130
gi 84703591   91 fmnp-dimGILEDAldr---gfDVLVLTNamkpmmrpritegLMALSddhkarlTLRVSMDHHdrahhdver------ge 160
gi 149735274  58 firt-dlkDIVRELykk---sdRIVISTNgff-------tdrIVDLCkef-pniGIRISIEGLeqtnneirg------ld 119
gi 4981355   166 ffwp-hlmDIFEEFkd-----sYFLVYSNgtli------keeTAKKLael-gnvTVSISVEGFetdtdwrr-------gr 225
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                       #                                           ##   
2YX0_A       223 erilrfLELMRDLp----------tRTVVRLTLVkgenm--------hspeKYAKLILkar-------pmfVEAKAYmfv 277
1TV8_A       143 ikattiLEQIDYAtsi-------glNVKVNVVIQkgind--------dqiiPMLEYFKdkh--------ieIRFIEFmdv 199
gi 1653098   168 gvfdkaVAAIKAAkakg-----frvTTNTTVFEGanv-----------akmQAFFDYLq-----------tLGIDGMmis 220
gi 77920251  146 gayadiRRGLELLmqagypaeglplGAQTVVCRQnide---------lpdmWRWLRDRhi----------iPYVELMtwq 206
gi 19887507  134 -dstvnRRAAEVLedsg-----mdlGFEMPAIPGeenwilevakladeygfDFLNVNEleftesnaeelrrRRFERVddd 207
gi 20094510  220 kvlelkKEAIKVLe----------rEGISTVLVPtlargv-----nddqirPMLDFARefev------irgINVQPIsft 278
gi 32363222  131 rvhtakLEAARAVtaa-------glPLTVNIVLHrgnidr------tgrmvDLAVDLGadri-----elanTQYYGWglr 192
gi 84703591  161 gsyaaaLMGIEWLar---------nGFSLAIAGRsiwg----------edeATARHGYgemletigvsldvMDPKRLvif 221
gi 149735274 120 dgynkgYTTLKKLremg----mkdvGFGMTVQDKnapd---------lvplYEISNEMgme-------fatASLHNSfyf 179
gi 4981355   226 gifkrvLEAWERLrrhg-----vifGASVTATRMnhdti-------mkdefWDFLEEQgvsy------vwvYQFMPVgmn 287
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
Feature 1                                                                                   
2YX0_A       278 gysrnrl---------------------------------------------------tinnmpshqDIREFAEA 301
1TV8_A       200 gndngw----------------------------------------------------dfskvvtkdEMLTMIEQ 222
gi 1653098   221 pgysyewapdqdhflkrdqtk-----------------------alfrellapwnkgkkawnfnhnpLFLDFLMG 272
gi 77920251  207 grarrhp--------------------------------------------------elevsvaemqGLFETLAA 231
gi 19887507  208 lsda---------------------------------------------------------vagserTALTALSE 225
gi 20094510  279 grtpreerermritipdfvk-------------------------lveeqtdgripaesfypvpiaaKIARLIGQ 328
gi 32363222  193 nraalmptaaqlaaareavrhartryaggpelvyvaadyyddrpkpcmdgwgstqltvtpagdvlpcPAAYAITT 267
gi 84703591  222 ae-------------------------------------------------------------mreeDDPPEITT 235
gi 149735274 180 veakniik-------------------------------------------------drpmvaknfeDLINELLR 205
gi 4981355   288 ptmdlvptpqqryerf--------------------------------hkleqlrlsgrfafvadfwNHGFLTNG 330

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