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


Conserved Protein Domain Family
DMB-PRT_CobT

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cd02439: DMB-PRT_CobT 
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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: 2-Oct-2020
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:
Feature 1         # ##                                             #      #   #                   
1JHQ_A         30 LKPPGSLGRLETLAVQLAGMPGlngtpqVGEKAVLVMCADHGVWd-EGVAVsp-kIVTAIQAAnmtRGTTGVCVLAAqa- 106 Salmonella ent...
1D0S_A         30 LKPPGSLGRLETLAVQLAGMPGlngtpqVGEKAVLVMCADHGVWd-EGVAVsp-kIVTAIQAAnmtRGTTGVCVLAAqa- 106 Salmonella typ...
YP_001030876   13 ESPMFALILSNSLVSTIEGVSGag---eSPAKSLMVPPLDAELIi-NGEITsv-dMTPNTPTGc-pTPAVLTLAMMDli- 85  Methanocorpusc...
YP_001689484    5 PDTLFALAAGATRTAAIEGISAag---aDPALMAHTPSADAELLt-YGHTVra-pVVPVSPSGc-pTPAVITRAVRElv- 77  Halobacterium ...
jgi:Hmuk_2245   5 GGTRLVLVAGSTRTAEIDGISAag---aDESLLAHTPAADAEILr-YGDVVra-pEVPQSPTGc-lTPAVVTRAVVEll- 77  Halomicrobium ...
YP_001491068   19 KKATFLLGCSVTKTCEIPNISQa----gIPQKLFLTPTLDAEFLciKQVKSl--pDIAKTPKGv-pTPAIITRAIHElkp 91  Arcobacter but...
ZP_05071132    17 GKADFLLAASVTRTCEIEGITQa----gIPGKIPLTPTLDAEFItnEKVFSm--pELAETPKGv-pTPALITRAVHKltp 89  Campylobactera...
P59919         48 LGFSLLLVLAGTRTAEVEGISAag---aTSAARRFTAVADAELLl-KGPDRprlcSLPPLPAGi--SPALISYVAARwi- 120 Prochlorococcu...
EEE40499       32 NNFKIFLVIAGTNTSQISGISAag---iNAKSRRKTALADAEFLl-KGASKdhkyKLPLLNAGv--TPALISHVCSKli- 104 Prochlorococcu...
ZP_01085845    23 PASQVLLLLAGTDTAEVPGISAag---aTPEVRRRTAAADAELLl-LGPSGlrphALPPLPAGv--SPALISHVVCRel- 95  Synechococcus ...
Feature 1                                                                                      ###
1JHQ_A        107 gaKVHVIDVGIDAEpipgvvnmrv---argcgniavGPAMSRLQAEALLLEVSrytcd-------laqrGVTLFGVGELG 176 Salmonella ent...
1D0S_A        107 gaKVHVIDVGIDAEpipgvvnmrv---argcgniavGPAMSRLQAEALLLEVSryacd-------laqrGVTLFGVGELG 176 Salmonella typ...
YP_001030876   86 gmKPLMIAAGLDHEvtvphiqf------gekaggdpREGRAVPNAKELFEKGRwlge--------ylsqTHDLLVLGECL 151 Methanocorpusc...
YP_001689484   78 gfESLVIDAGLAEPtgaptvtt------gispgadiRDETPVPDAEAAYSAAYefg----------hglHTDELVIAETI 141 Halobacterium ...
jgi:Hmuk_2245  78 dlDVTVVDGGLAEPsgaptvtv------garpgrdvREQDPVPSAPGAFEAARqfg----------rslPADEVVIGETI 141 Halomicrobium ...
YP_001491068   92 fsNIEILNLGLEVVpqieyfkihnfdinpsnsidknANIPAMETFQKGIEFAQsy------------etKDDYIILAETI 159 Arcobacter but...
ZP_05071132    90 ysNIEVLNLGLDAVpqktpiqsfd--iypsgsvasgANIDARTVFEKGMIAGKny------------elKGNYLILAEST 155 Campylobactera...
P59919        121 gvDPLVAAVGLTLSppfphlrlevp-gmgpaaclstGEAMGLSRVHALWQRGFclg-----------rgLRRPLVLAECV 188 Prochlorococcu...
EEE40499      105 niDPVIVPLGLGVKpyfnhlvvedr-dlgpsnclttGKSMSKKRVINLYEKGLaig-----------ksSKQPILISESV 172 Prochlorococcu...
ZP_01085845    96 alVPLVADLGCAVApavphlrlg----gtparclssGAAMPRQRVERLLRLGQrwaarwvaarhdtatgEPAPVLIAECV 171 Synechococcus ...
Feature 1         ####                                                                            
1JHQ_A        177 MANTTPAAAMVSVFTGsdakEVVGIGANLPpsrIDNKVDVVRRAIAINqpn-------prDGIDVLSKVGGFDLVGMTGV 249 Salmonella ent...
1D0S_A        177 MANTTPAAAMVSVFTGsdakEVVGIGANLPpsrIDNKVDVVRRAIAINqpn-------prDGIDVLSKVGGFDLVGMTGV 249 Salmonella typ...
YP_001030876  152 PGGTTTALCVLRALGYq--aKVSSCLVDNP---VCIKEKIAAEAVKKVqka------gvtDPLEIVSMVGDPMIPVAAGI 220 Methanocorpusc...
YP_001689484  142 PGGTTTAMGVLAALGEp--rIVSSSLPNNP---VALKERVVDDALAASgleqg---dlagEPVAAVRQMGDPVLAVVAGL 213 Halobacterium ...
jgi:Hmuk_2245 142 PGGTTTALGVLRALGEr--gGVSSSLPENP---VDQKESVVEEGLTASamepg---eaadQPKRAVRRMGDPVLAVAAGV 213 Halomicrobium ...
YP_001491068  160 PAGTTTANATAKALGYdcdgYFSSSFKNNP---NDIKEKTIKNALANIns--------ndDLFDKLSKVSDNMIIFCAGF 228 Arcobacter but...
ZP_05071132   156 PGGTTTATTTALALGYdcrnDFSSSFLNSP---DSIKEKTINEALSLLde--------dmTNFEKLSLVSDNMLIFYAGF 224 Campylobactera...
P59919        189 PGGTTTAQAVLTGLGLqvadLISGSARQAP---MILKQELVDRGLSKAalg------fnpPPQRVIAALGDPFQPVAVGL 259 Prochlorococcu...
EEE40499      173 PGGTTTAQAVMEAFGLrvanLVGSSLFKAP---RELRKKVVQKGLLNAnlk------tdfDSFDVVAAVGDPFQAFSMGL 243 Prochlorococcu...
ZP_01085845   172 PGGTSTAQAVLTGLGVeaagLVSGSLRQPA---HALKRELTARGLAAAaagpvpgallalDPQAVLAAVGDPMQALAAGV 248 Synechococcus ...
Feature 1                       ###                               #                               
1JHQ_A        250 MLGAArcgLPVLLDGFLSYSAALAACQiap-------avrPYLIPSHFSAe----------KGARIALAHLS-------- 304 Salmonella ent...
1D0S_A        250 MLGAArcgLPVLLDGFLSYSAALAACQiap-------avrPYLIPSHFSAe----------KGARIALAHLS-------- 304 Salmonella typ...
YP_001030876  221 AEGYR---GKLFLAGGTQMLAAAAVIRalg--------ntVPDIVTTVYVydd------ktASFKETAAAVGadayyvd- 282 Methanocorpusc...
YP_001689484  214 AAGALdagIDVTLAGGTQLATAGALVRhdg-------vtePMTLATTSFVagd------dsAGIDALAADQDlavtvtdp 280 Halobacterium ...
jgi:Hmuk_2245 214 AIGAIetgRAVTLAGGTQLATVGALLRhag-------iegPLSLATTSFVddd------psADVRGLAADLDldltvtd- 279 Halomicrobium ...
YP_001491068  229 ILGSQnknLKIVLAGGTQMACVLLVVNsilksmdgvldssNLALFTTKWIked------knSNIKALLEQLDfpinayss 302 Arcobacter but...
ZP_05071132   225 LLEASr-rFHVVLAGGTQMAACLLVADklkedvlmriksdNITLATTSWVand------enSDIKHILSLLSytphavht 297 Campylobactera...
P59919        260 LLGAReagQPVMLGGGSQMVAVLALALaamepshrqdmvdGIVLGTTSWLaeeakrsdgrpGALECLIDCVGeffgvrll 339 Prochlorococcu...
EEE40499      244 LIGARlakQSVILSGGSQMLAIILLVLefldvkneddfieDVFIATTGWLik--------dNSLNDLLNIINekydvkll 315 Prochlorococcu...
ZP_01085845   249 LLGAAgrrVPVLLAGGSQMAAVLALALalapahqrpclaeYGALATTAWVaqe------pgSDLSLLLERLGerwgvrpm 322 Synechococcus ...
Feature 1                                ###                          #    
1JHQ_A        305 ------------MEPYLHMAM-RLGE--GSGAALAMPIVEAACAMFh--nMGELAAS 344 Salmonella enterica
1D0S_A        305 ------------MEPYLHMAM-RLGE--GSGAALAMPIVEAACAMFh--nMGELAAS 344 Salmonella typhimurium
YP_001030876  283 -----pefgsigHDGLARYAEgEIKEgsGAGGAMFLASILGFPPEVi---RNTIREQ 331 Methanocorpusculum labreanum Z
YP_001689484  281 -----afearesHPAMAAYLDgEAKEgvGMGGALALAAEAGIGMDSv---RNAIISV 329 Halobacterium salinarum R1
jgi:Hmuk_2245 280 -----pafdradHVAMERFVVgEAKEgvGMGGALALADRAELDPAVvrdrVAAIADD 331 Halomicrobium mukohataei DSM 12286
YP_001491068  303 ----dfdfslssHPALKLYDEgEAKEgvGCGGALCYASINGLSKQIv---TKKIEEF 352 Arcobacter butzleri RM4018
ZP_05071132   298 ----sfsfadteIPVLKLYDEgEAKEgvGAGAALAYANTNGTTNKEl---LDAIELL 347 Campylobacterales bacterium GD 1
P59919        340 glatglrfnnsqHRALQDYELgYVKEgvGAGALALLAQLQGASCEQl---LEACDQA 393 Prochlorococcus marinus str. MIT 9313
EEE40499      316 glasplnfkfskYKELKDYELgHVKEgvGAGGISLLAFLDGFKNEEi---VSLCQQN 369 Prochlorococcus marinus str. MIT 9202
ZP_01085845   323 afasslrfghcrSAALRDYERgYVKEgvGAGGLALLWELSGRSTGAl---AAACDQA 376 Synechococcus sp. WH 5701

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