1JHQ,1WX1,1WX1,1JHA,1D0S,1D0V


Conserved Protein Domain Family
DMB-PRT_CobT

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cd02439: DMB-PRT_CobT 
Click on image for an interactive view with Cn3D
Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT), also called CobT.
Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (DMB-PRT/CobT, not to be confused with the CobT subunit of cobaltochelatase, which does not belong to this group) catalyzes the synthesis of alpha-ribazole-5'-phosphate, from nicotinate mononucleotide (NAMN) and 5,6-dimethylbenzimidazole (DMB). This function is essential to the anaerobic biosynthesis pathway of cobalamin (vitamin B12), which is the largest and most complex cofactor in a number of enzyme-catalyzed reactions in bacteria, archaea and eukaryotes. Only eubacteria and archaebacteria can synthesize vitamin B12; multicellular organisms have lost this ability during evolution. DMB-PRT/CobT works sequentially with CobC (a phosphatase) to couple the lower ligand of cobalamin to a ribosyl moiety. DMB is the most common lower ligand of cobamides; other lower ligands include adenine, 5-methoxybenzimidazole or phenol. It has been suggested that earlier metabolic or enzymatic steps may control which lower ligand is available to DMB-PRT/CobT. In Salmonella enterica, for example, the lower ligand is DMB under aerobic conditions and adenine or 2-methyladenine under anaerobic conditions. Salmonella enterica DMB-PRT/CobT is a homodimer with two active sites, each active site is comprised of residues from both monomers. This group includes two distinct subfamilies, one archaeal-like, the other comprised of bacterial sequences.
Statistics
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PSSM-Id: 143332
View PSSM: cd02439
Aligned: 160 rows
Threshold Bit Score: 138.004
Threshold Setting Gi: 169236284
Created: 20-Apr-2005
Updated: 17-Jan-2013
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 21 residues -Click on image for an interactive view with Cn3D
Feature 1:active site pocket [active site]
Evidence:
  • Comment:based on Salmonella enterica and Salmonella typhimurium CobT bound with various bases and their reaction product
  • Comment:CobT is a homodimer with two active sites, each active site is comprised of residues from both monomers.
  • Structure:1D0S_A; Salmonella typhimurium CobT monomer binds DMB, contacts at 4A.
    View structure with Cn3D
  • Structure:1D0V_A; Salmonella typhimurium CobT monomer binds nicotinate and alpha-ribazole-5prime-phosphate (the products of the reaction of DMB with NaMN), contacts at 4A.
    View structure with Cn3D
  • Structure:1JHA_A; Salmonella enterica CobT monomer binds nicotinate and adenosine monophosphate (the products of the reaction of adenine with NaMN), contacts at 4A.
    View structure with Cn3D
  • Structure:1JHQ_A; Salmonella enterica CobT monomer binds nicotinate and N1-(5'-phospho -alpha -ribosyl)-5-methoxybenzimidazole (the products of the reaction of 5-methoxybenzimidazole with NaMN), contacts at 4A.
    View structure with Cn3D
  • Structure:1WX1_A,Thermus thermophilus CobT homodimer with both active sites highlighted.
    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        # ##                                             #      #   #                   
1JHQ_A        30 LKPPGSLGRLETLAVQLAGMPGlngtpqVGEKAVLVMCADHGVWd-EGVAVsp-kIVTAIQAAnmtRGTTGVCVLAAqa- 106
1D0S_A        30 LKPPGSLGRLETLAVQLAGMPGlngtpqVGEKAVLVMCADHGVWd-EGVAVsp-kIVTAIQAAnmtRGTTGVCVLAAqa- 106
gi 124486260  13 ESPMFALILSNSLVSTIEGVSGag---eSPAKSLMVPPLDAELIi-NGEITsv-dMTPNTPTGc-pTPAVLTLAMMDli- 85
gi 169236284   5 PDTLFALAAGATRTAAIEGISAag---aDPALMAHTPSADAELLt-YGHTVra-pVVPVSPSGc-pTPAVITRAVRElv- 77
gi 257170599   5 GGTRLVLVAGSTRTAEIDGISAag---aDESLLAHTPAADAEILr-YGDVVra-pEVPQSPTGc-lTPAVVTRAVVEll- 77
gi 157738384  19 KKATFLLGCSVTKTCEIPNISQa----gIPQKLFLTPTLDAEFLciKQVKSl--pDIAKTPKGv-pTPAIITRAIHElkp 91
gi 254457704  17 GKADFLLAASVTRTCEIEGITQa----gIPGKIPLTPTLDAEFItnEKVFSm--pELAETPKGv-pTPALITRAVHKltp 89
gi 37999947   48 LGFSLLLVLAGTRTAEVEGISAag---aTSAARRFTAVADAELLl-KGPDRprlcSLPPLPAGi--SPALISYVAARwi- 120
gi 221538046  32 NNFKIFLVIAGTNTSQISGISAag---iNAKSRRKTALADAEFLl-KGASKdhkyKLPLLNAGv--TPALISHVCSKli- 104
gi 87303041   23 PASQVLLLLAGTDTAEVPGISAag---aTPEVRRRTAAADAELLl-LGPSGlrphALPPLPAGv--SPALISHVVCRel- 95
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                                                                                     ###
1JHQ_A       107 gaKVHVIDVGIDAEpipgvvnmrv---argcgniavGPAMSRLQAEALLLEVSrytcd-------laqrGVTLFGVGELG 176
1D0S_A       107 gaKVHVIDVGIDAEpipgvvnmrv---argcgniavGPAMSRLQAEALLLEVSryacd-------laqrGVTLFGVGELG 176
gi 124486260  86 gmKPLMIAAGLDHEvtvphiqf------gekaggdpREGRAVPNAKELFEKGRwlge--------ylsqTHDLLVLGECL 151
gi 169236284  78 gfESLVIDAGLAEPtgaptvtt------gispgadiRDETPVPDAEAAYSAAYefg----------hglHTDELVIAETI 141
gi 257170599  78 dlDVTVVDGGLAEPsgaptvtv------garpgrdvREQDPVPSAPGAFEAARqfg----------rslPADEVVIGETI 141
gi 157738384  92 fsNIEILNLGLEVVpqieyfkihnfdinpsnsidknANIPAMETFQKGIEFAQsy------------etKDDYIILAETI 159
gi 254457704  90 ysNIEVLNLGLDAVpqktpiqsfd--iypsgsvasgANIDARTVFEKGMIAGKny------------elKGNYLILAEST 155
gi 37999947  121 gvDPLVAAVGLTLSppfphlrlevp-gmgpaaclstGEAMGLSRVHALWQRGFclg-----------rgLRRPLVLAECV 188
gi 221538046 105 niDPVIVPLGLGVKpyfnhlvvedr-dlgpsnclttGKSMSKKRVINLYEKGLaig-----------ksSKQPILISESV 172
gi 87303041   96 alVPLVADLGCAVApavphlrlg----gtparclssGAAMPRQRVERLLRLGQrwaarwvaarhdtatgEPAPVLIAECV 171
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1        ####                                                                            
1JHQ_A       177 MANTTPAAAMVSVFTGsdakEVVGIGANLPpsrIDNKVDVVRRAIAINqpn-------prDGIDVLSKVGGFDLVGMTGV 249
1D0S_A       177 MANTTPAAAMVSVFTGsdakEVVGIGANLPpsrIDNKVDVVRRAIAINqpn-------prDGIDVLSKVGGFDLVGMTGV 249
gi 124486260 152 PGGTTTALCVLRALGYq--aKVSSCLVDNP---VCIKEKIAAEAVKKVqka------gvtDPLEIVSMVGDPMIPVAAGI 220
gi 169236284 142 PGGTTTAMGVLAALGEp--rIVSSSLPNNP---VALKERVVDDALAASgleqg---dlagEPVAAVRQMGDPVLAVVAGL 213
gi 257170599 142 PGGTTTALGVLRALGEr--gGVSSSLPENP---VDQKESVVEEGLTASamepg---eaadQPKRAVRRMGDPVLAVAAGV 213
gi 157738384 160 PAGTTTANATAKALGYdcdgYFSSSFKNNP---NDIKEKTIKNALANIns--------ndDLFDKLSKVSDNMIIFCAGF 228
gi 254457704 156 PGGTTTATTTALALGYdcrnDFSSSFLNSP---DSIKEKTINEALSLLde--------dmTNFEKLSLVSDNMLIFYAGF 224
gi 37999947  189 PGGTTTAQAVLTGLGLqvadLISGSARQAP---MILKQELVDRGLSKAalg------fnpPPQRVIAALGDPFQPVAVGL 259
gi 221538046 173 PGGTTTAQAVMEAFGLrvanLVGSSLFKAP---RELRKKVVQKGLLNAnlk------tdfDSFDVVAAVGDPFQAFSMGL 243
gi 87303041  172 PGGTSTAQAVLTGLGVeaagLVSGSLRQPA---HALKRELTARGLAAAaagpvpgallalDPQAVLAAVGDPMQALAAGV 248
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
Feature 1                      ###                               #                               
1JHQ_A       250 MLGAArcgLPVLLDGFLSYSAALAACQiap-------avrPYLIPSHFSAe----------KGARIALAHLS-------- 304
1D0S_A       250 MLGAArcgLPVLLDGFLSYSAALAACQiap-------avrPYLIPSHFSAe----------KGARIALAHLS-------- 304
gi 124486260 221 AEGYR---GKLFLAGGTQMLAAAAVIRalg--------ntVPDIVTTVYVydd------ktASFKETAAAVGadayyvd- 282
gi 169236284 214 AAGALdagIDVTLAGGTQLATAGALVRhdg-------vtePMTLATTSFVagd------dsAGIDALAADQDlavtvtdp 280
gi 257170599 214 AIGAIetgRAVTLAGGTQLATVGALLRhag-------iegPLSLATTSFVddd------psADVRGLAADLDldltvtd- 279
gi 157738384 229 ILGSQnknLKIVLAGGTQMACVLLVVNsilksmdgvldssNLALFTTKWIked------knSNIKALLEQLDfpinayss 302
gi 254457704 225 LLEASr-rFHVVLAGGTQMAACLLVADklkedvlmriksdNITLATTSWVand------enSDIKHILSLLSytphavht 297
gi 37999947  260 LLGAReagQPVMLGGGSQMVAVLALALaamepshrqdmvdGIVLGTTSWLaeeakrsdgrpGALECLIDCVGeffgvrll 339
gi 221538046 244 LIGARlakQSVILSGGSQMLAIILLVLefldvkneddfieDVFIATTGWLik--------dNSLNDLLNIINekydvkll 315
gi 87303041  249 LLGAAgrrVPVLLAGGSQMAAVLALALalapahqrpclaeYGALATTAWVaqe------pgSDLSLLLERLGerwgvrpm 322
                        330       340       350       360       370
                 ....*....|....*....|....*....|....*....|....*....|....*..
Feature 1                               ###                          #    
1JHQ_A       305 ------------MEPYLHMAM-RLGE--GSGAALAMPIVEAACAMFh--nMGELAAS 344
1D0S_A       305 ------------MEPYLHMAM-RLGE--GSGAALAMPIVEAACAMFh--nMGELAAS 344
gi 124486260 283 -----pefgsigHDGLARYAEgEIKEgsGAGGAMFLASILGFPPEVi---RNTIREQ 331
gi 169236284 281 -----afearesHPAMAAYLDgEAKEgvGMGGALALAAEAGIGMDSv---RNAIISV 329
gi 257170599 280 -----pafdradHVAMERFVVgEAKEgvGMGGALALADRAELDPAVvrdrVAAIADD 331
gi 157738384 303 ----dfdfslssHPALKLYDEgEAKEgvGCGGALCYASINGLSKQIv---TKKIEEF 352
gi 254457704 298 ----sfsfadteIPVLKLYDEgEAKEgvGAGAALAYANTNGTTNKEl---LDAIELL 347
gi 37999947  340 glatglrfnnsqHRALQDYELgYVKEgvGAGALALLAQLQGASCEQl---LEACDQA 393
gi 221538046 316 glasplnfkfskYKELKDYELgHVKEgvGAGGISLLAFLDGFKNEEi---VSLCQQN 369
gi 87303041  323 afasslrfghcrSAALRDYERgYVKEgvGAGGLALLWELSGRSTGAl---AAACDQA 376

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