2YX0,2A5H,1TV8,2Z2U,1OLT,1R30,2QGQ


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:
Feature 1              # # # ###                                                           # ## 
2YX0_A       74 MTPvlaWCTHNCIFCWrpmenflgtelpqpwddpafiveesikaqrklligykgnpkvdkkkfeeawnPTHAAIsLSGEP 153 Pyrococcus horik...
1TV8_A       18 LSVt-dRCNFRCDYCMpkevfgddfvflpknel------------------ltfdemariakvyaelgVKKIRI-TGGEP 77  Staphylococcus a...
BAA18014     54 LEPl-fRCNLACQGCGkiqhpteilkqnl--------------------------spedcfraveecgAPVVSI-PGGEP 105 Synechocystis sp...
YP_358066    29 LELs-rQCDLRCLYCYadsgtaladelals------------------------eiyavleqamalgiRRVVVL-GGGEP 82  Pelobacter carbi...
AAM02200     21 VFVt-gVCNRGCWYCPvsprkkgsdvsfaner--------------------pirserdlvkeaelmdAEGASL-TGGDP 78  Methanopyrus kan...
NP_614357    97 IDVt-nRCNMNCPVCFanaeakgyvyepsleq---------------------ieemldllrserpvpAPAVQF-AGGEP 153 Methanopyrus kan...
P59749       14 IELt-hRCPLHCPYCSnplelvrreaeltc------------------------eqwtdiltqarelgVVQMHF-SGGEP 67  Streptomyces rochei
ZP_01017419  36 LNTg-tLCNIACENCYilsspqnddlvylsr-----------------------dearpyldearemgAREIGI-TGGEP 90  Parvularcula ber...
EDM51160     10 VIVt-yRCNARCSMCNrykapskpeee------------------------------isietikklpkMYFTNI-TGGEP 57  Eubacterium vent...
AAD35906    114 LSPt-yACNLNCVGCYaglygrkyelshd--------------------------evrdilkqandlgIYFFII-TGGEP 165 Thermotoga marit...
Feature 1                                 ###                             #                     
2YX0_A      154 mlyp-ymgDLVEEFhkr---gfTTFIVTNgtipe----rleeMIKEDkl---ptQLYVSITAPdietynsvnipmipdgw 222 Pyrococcus horik...
1TV8_A       78 lmr--rdlDVLIAKlnqidgieDIGLTTNgll-------lkkHGQKLyda-glrRINVSLDAIddtlfqsin-----nrn 142 Staphylococcus a...
BAA18014    106 llhp-qidEIVRGLvar---rkFIYLCTNail-------lekSLDKFqps-pylTFSVHLDGPrehhdkcvd------rq 167 Synechocystis sp...
YP_358066    83 lmyp-hvvEIMQYLaqh---giGIDLFTNgtqi------taeLAQEFvrl--gvAPVVKMNSRrqqvqdfla-----grq 145 Pelobacter carbi...
AAM02200     79 ltrleravNIIRTLkdefgddfHIHLYAPa-----------eSVREGai---eeLDGVGLDELrvhpsp----------- 133 Methanopyrus kan...
NP_614357   154 lvre-divEIVAAAder---gfHVQIATNgvefa----rnpeLAEDLhaa-glnVVYLQFDGLnpeiyeeir-----gsr 219 Methanopyrus kan...
P59749       68 larp-dlpDLVGHArrl---gaYVNLVTSgvgl------taeRAHDLarr-gvdHVQLSLQDAdpaagqaia------ga 130 Streptomyces rochei
ZP_01017419  91 fmnp-dimGILEDAldr---gfDVLVLTNamkpmmrpritegLMALSddhkarlTLRVSMDHHdrahhdver------ge 160 Parvularcula ber...
EDM51160     58 firt-dlkDIVRELykk---sdRIVISTNgff-------tdrIVDLCkef-pniGIRISIEGLeqtnneirg------ld 119 Eubacterium vent...
AAD35906    166 ffwp-hlmDIFEEFkd-----sYFLVYSNgtli------keeTAKKLael-gnvTVSISVEGFetdtdwrr-------gr 225 Thermotoga marit...
Feature 1                                      #                                           ##   
2YX0_A      223 erilrfLELMRDLp----------tRTVVRLTLVkgenm--------hspeKYAKLILkar-------pmfVEAKAYmfv 277 Pyrococcus horik...
1TV8_A      143 ikattiLEQIDYAtsi-------glNVKVNVVIQkgind--------dqiiPMLEYFKdkh--------ieIRFIEFmdv 199 Staphylococcus a...
BAA18014    168 gvfdkaVAAIKAAkakg-----frvTTNTTVFEGanv-----------akmQAFFDYLq-----------tLGIDGMmis 220 Synechocystis sp...
YP_358066   146 gayadiRRGLELLmqagypaeglplGAQTVVCRQnide---------lpdmWRWLRDRhi----------iPYVELMtwq 206 Pelobacter carbi...
AAM02200    134 -dstvnRRAAEVLedsg-----mdlGFEMPAIPGeenwilevakladeygfDFLNVNEleftesnaeelrrRRFERVddd 207 Methanopyrus kan...
NP_614357   220 kvlelkKEAIKVLe----------rEGISTVLVPtlargv-----nddqirPMLDFARefev------irgINVQPIsft 278 Methanopyrus kan...
P59749      131 rvhtakLEAARAVtaa-------glPLTVNIVLHrgnidr------tgrmvDLAVDLGadri-----elanTQYYGWglr 192 Streptomyces rochei
ZP_01017419 161 gsyaaaLMGIEWLar---------nGFSLAIAGRsiwg----------edeATARHGYgemletigvsldvMDPKRLvif 221 Parvularcula ber...
EDM51160    120 dgynkgYTTLKKLremg----mkdvGFGMTVQDKnapd---------lvplYEISNEMgme-------fatASLHNSfyf 179 Eubacterium vent...
AAD35906    226 gifkrvLEAWERLrrhg-----vifGASVTATRMnhdti-------mkdefWDFLEEQgvsy------vwvYQFMPVgmn 287 Thermotoga marit...
Feature 1                                                                                  
2YX0_A      278 gysrnrl---------------------------------------------------tinnmpshqDIREFAEA 301 Pyrococcus horikoshii...
1TV8_A      200 gndngw----------------------------------------------------dfskvvtkdEMLTMIEQ 222 Staphylococcus aureus
BAA18014    221 pgysyewapdqdhflkrdqtk-----------------------alfrellapwnkgkkawnfnhnpLFLDFLMG 272 Synechocystis sp. PCC...
YP_358066   207 grarrhp--------------------------------------------------elevsvaemqGLFETLAA 231 Pelobacter carbinolic...
AAM02200    208 lsda---------------------------------------------------------vagserTALTALSE 225 Methanopyrus kandleri...
NP_614357   279 grtpreerermritipdfvk-------------------------lveeqtdgripaesfypvpiaaKIARLIGQ 328 Methanopyrus kandleri...
P59749      193 nraalmptaaqlaaareavrhartryaggpelvyvaadyyddrpkpcmdgwgstqltvtpagdvlpcPAAYAITT 267 Streptomyces rochei
ZP_01017419 222 ae-------------------------------------------------------------mreeDDPPEITT 235 Parvularcula bermuden...
EDM51160    180 veakniik-------------------------------------------------drpmvaknfeDLINELLR 205 Eubacterium ventriosu...
AAD35906    288 ptmdlvptpqqryerf--------------------------------hkleqlrlsgrfafvadfwNHGFLTNG 330 Thermotoga maritima MSB8

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