1DZR,1RTV,1EP0,6C46,1WLT,3RYK,2C0Z,1PM7,4HN0,1OFN,1NYW,4HMZ,5BUV,1NXM


Conserved Protein Domain Family
cupin_RmlC

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cd00438: cupin_RmlC 
RmlC carbohydrate epimerase, involved in dTDP-L-rhamnose production
RmlC (deoxythymidine diphosphate (dTDP)-4-keto-6-deoxy-D-hexulose 3, 5-epimerase or dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase; also known as RfbC) is a carbohydrate epimerase involved in the production of dTDP-L-rhamnose, a precursor of the bacterial cell wall constituent, L-rhamnose. L-Rhamnose (6-deoxy-l-mannose) plays an important role in the cell-wall structure of many bacterial species. It has been found to contribute to the virulence of several species, including the Gram-negative Salmonella enterica and Vibrio cholerae, where it is present as a part of the O-antigen, and is essential for the growth of Gram-positive bacteria such as Streptococcus pyogenes. RmlC converts dTDP-6-deoxy-D-xylo-4-hexulose to dTDP-6-deoxy-L-xylo-hexulose by catalyzing the epimerization of the 5-methyl and 3-hydroxyl groups of hexulose, the third of four steps in the dTDP-L-rhamnose biosynthetic pathway. RmlC belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization.
Statistics
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PSSM-Id: 380337
Aligned: 178 rows
Threshold Bit Score: 169.14
Created: 6-Mar-2002
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 8 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:The RmlC active site is located at the homodimeric interface and both subunits contribute residues to the active site.
  • Structure:1NYW: Streptococcus suis RmlC epimerase binds deoxythymidine; contacts at 4.0A

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                              # #          # #       #  
1DZR_A         4 VIKTAi-pDVLILEPKVFGDe---RGFFFESYNqQTFEELigrk----vtfvQDNHSKSKknVLRGLHFQrgenaQGKLV 75  Salmonella typh...
1NYW_A        12 ARPVEaipGMLEFDIPVHGDn---RGWFKENFQkEKMLPLgfpesffaegklQNNVSFSRknVLRGLHAEp----WDKYI 84  Streptococcus suis
1NXM_A        12 ARPVEaipGMLEFDIPVHGDn---RGWFKENFQkEKMLPLgfpesffaegklQNNVSFSRknVLRGLHAEp----WDKYI 84  Streptococcus suis
EKX91543      14 LHELSl-pGVFLAKPTIHSDe---RGTFQEWFKaSTFEEAtgfp----ldmqQGNLSTSRrgVVRGLHYAdvppgQAKYV 85  Corynebacterium...
AHI03954       1 MVELPi-pGAWVFVPRVFGDe---RGSFHEWFRaEQFTEHlgyp----ftvaQANLSRSAknVVRGIHLAevppgQAKFV 72  Corynebacterium...
ABB69763       3 IKEMAi-aGAFRIIPDKYHDc---RGCFFEAFRiEELRRAtgfp----fqvrQGNVSVSRrsTIRGVHGTggdsgEAKLI 74  Streptomyces sp...
SDD27770       4 VTRGRv-pGVLVLEPHRLTDe---RGVFYEGVRtDALTAVtgrp----fvprQVNYSVSRrgTLRGLHGVkvppgQAKLV 75  Streptomyces sp...
CAA09646       3 IQELRevpGAYVITPRQWPDp---RGTFFESLRtDLVSEAvgrp----fevrQINYSTSRrnTLRGVHGVlippgQAKYV 75  Streptomyces vi...
AAS07755      11 VQPLAi-dGAHVVTSQSFGDe---RGDFFEVYRqDVLTEAlgyr----prflQTNVSTSCrnVVRGVHGAmtppgLAKFV 82  Amycolatopsis m...
XP_001328402   8 FTPLKv-kDAGVVTLAEHVSdldiTVDCFECLK-SPPATQm----------pQITVSRSQknVIRGLHCSp----HHKLV 71  Trichomonas vag...
Feature 1                                                      #            #                    
1DZR_A        76 RCAV-GEVFDVAVDIRkespTFGQWVGVNLSae-nkRQLWIPeGFAHGFVTLSeyAEFLYKATNYYSPs---sEGSILWN 150 Salmonella typh...
1NYW_A        85 SVADgGKVLGTWVDLReg-eTFGNTYQTVIDa---sKSIFVPrGVANGFQVLSdfVAYSYLVNDYWALelkpkYAFVNYA 160 Streptococcus suis
1NXM_A        85 SVADgGKVLGTWVDLReg-eTFGNTYQTVIDa---sKSIFVPrGVANGFQVLSdfVAYSYLVNDYWALelkpkYAFVNYA 160 Streptococcus suis
EKX91543      86 TCVA-GSIRDVVVDVRlgspTFGQHVAVELSae-nrHAVFVPvGFAHGFAALSd-ATVMYVTTSEYDPe---iERELNPC 159 Corynebacterium...
AHI03954      73 TCVS-GVITDILVDLRvgspTFGKHVSVELSed-nnFGLFVPlGVGHGFAAQSerATVSYLVTEAYNPe---rEFEVDAY 147 Corynebacterium...
ABB69763      75 SCAR-GAVLDVVVDLRvgspVFGTFEAAPLTedsgeLIFLVP-GLGHAYQALTddTRITYLCAERFVPg---sQIDINPL 149 Streptomyces sp...
SDD27770      76 TCVR-GSVRDVVVDLRlgspEFGTYETTALDae-sgRAVYVPeGVVHGFLALTddACVSYLLSTPHVPg---tQIDIDPL 150 Streptomyces sp...
CAA09646      76 TCVR-GALRDMVVDLRvgspTFGQSASTLLTpe-ngVAVHVAeGLGHGFLALTddTCISYALSTAHVPg---tQFEIDPL 150 Streptomyces vi...
AAS07755      83 TCLR-GSLLDFVVDVRtgspTFGQWDMIVLNqh-ggTAVYVEeGLGHAFVSLEddTCVQYLLSDLYRPa---eVLTVQPL 157 Amycolatopsis m...
XP_001328402  72 QCPT-GKAFDVVVDLRpdspTFLQWDGHWIDr---tHHMFIPpFCAHGFFASEddTAILYLQGGCFAPe---lDFSLNYL 144 Trichomonas vag...
Feature 1                               #   
1DZR_A       151 deaigIEWPfs----qlPELSaKDAAA 173 Salmonella typhimurium
1NYW_A       161 dpsldIKWEnl----eeAEVSeADENH 183 Streptococcus suis
1NXM_A       161 dpsldIKWEnl----eeAEVSeADENH 183 Streptococcus suis
EKX91543     160 dpalaIEWGva-----ePIMSeKDVAA 181 Corynebacterium durum F0235
AHI03954     148 dadlaIDWPvda---dqAVLSeKDTKA 171 Corynebacterium falsenii DSM 44353
ABB69763     150 dqelaLPWDls----eePVISdKDRAA 172 Streptomyces sp. Tu6071
SDD27770     151 dpdlaIAWTagapadleLLLSaKDRAA 177 Streptomyces sp. LaPpAH-199
CAA09646     151 dpdlaLPWGfd----epPLLSaKDAGA 173 Streptomyces violaceoruber
AAS07755     158 dp--eIGLPlnl--pgePILSeRDAAA 180 Amycolatopsis mediterranei S699
XP_001328402 145 dktvnVDWPkpid-addYVISpKDRGN 170 Trichomonas vaginalis G3

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