TABLE 2

GRM locus shell protein oligomer properties based on homology modelinga

LocusPredicted functionMetabolites predicted to cross the shellShell protein typePore motif residues (diam [Å])Pore propertiesModel in Fig. 3Closest homolog characterizedb (% identity)
GRM1Choline degradationCholine, trimethylamine, ethanol, acetyl-phosphateBMC-HY-V-G-G (4.7)Positive2PduJ (76)
BMC-HG-X-C-P-QOccluded (Fe-S cluster)NAcGrpU (>50d)
BMC-HR-F-T/SOccluded, possibly gated negatively charged β-barrel3PduU (61)
BMC-HN-I/V-A/G-S (4.5)Polar, neutral/negative1PduA (56)
BMC-TS/P-T/V-C-POccluded (Fe-S cluster)NAPduT (40)
GRM2Choline degradationCholine, trimethylamine, ethanol, acetyl-phosphateBMC-HK-V-G-S (4.5)Positive5PduA (51)
BMC-HN-V/I-G-S (4.3)Polar, neutral/negative4PduJ (66)
BMC-TNANANANA
GRM3Propanediol degradationPropanediol, propanol, propionyl-phosphateBMC-HK-I-G-S (4.3)Positive6PduA (85)
BMC-HG-X-C-P-QOccluded (Fe-S cluster)NAGrpU (>50d)
BMC-HL/F-T/A-K/R-G-G/DOccluded7None
BMC-TG-A/G-G-H (3.7)Negative (3 pores)13PduB (67)
GRM4Propanediol degradationPropanediol, propanol, propionyl-phosphateBMC-HK-I-G-S (4.7)Positive8PduJ (82)
BMC-HR-T-I-G-SOccluded9PduK (49)
BMC-TG-A-G-HNegative (3 pores)13PduB (77)
GRM5Fuculose- and/or rhamnulose-1-phosphate degradation via propanediolFuculose- and/or rhamnulose-1-phosphate, DHAP,e (propanol),f propionyl-phosphateBMC-HR/K-N-K-P-AOccludedg11CcmK1/2 (35)g
BMC-HK-I-G-S (4.4)Positive10PduA (79)
BMC-HR-K-L-G-GOccluded12PduJ (40)
BMC-TT-V-C-POccluded (Fe-S cluster)NAPduT (40)
  • a See Data Set S1 in the supplemental material for the complete data set.

  • b The closest homolog characterized by BLAST analysis. The representative shell proteins depicted in Fig. 3 were searched against PDU, EUT, carboxysome, and Planctomycetes and Verrucomicrobia microcompartment shell proteins in Salmonella enterica, Synechococcus elongatus PCC7942, Halothiobacillus neapolitanus, and Planctomyces limnophilus.

  • c NA, not applicable.

  • d The percent identities are to the GrpU orthologs in the Protein Data Bank.

  • e DHAP, dihydroxyacetone phosphate.

  • f Production of propanol is not necessarily required for NAD+ regeneration in GRM5, because of the proposed function of a lactaldehyde reductase.

  • g In the model, the predicted positively charged pores are occluded (Fig. 3, model 11), but note that the best available structural template (CcmK1 from Thermosynechococcus elongatus) is only 35% identical.