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Conserved domains on  [gi|1632924774|gb|TKE04096|]
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propanediol utilization microcompartment protein PduU [Escherichia coli]

Protein Classification

similar to ethanolamine utilization protein EutS( domain architecture ID 10790903)

protein similar to ethanolamine utilization protein EutS

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
EutS COG4810
Ethanolamine utilization protein EutS, microcompartment shell protein [Amino acid transport ...
 1-116 2.74e-66

Ethanolamine utilization protein EutS, microcompartment shell protein [Amino acid transport and metabolism];


:

Pssm-ID: 443838  Cd Length: 117  Bit Score: 195.46  E-value: 2.74e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632924774   1 MTTQHTTERMIQEYVPGKQVTLAHVIANPGKDLFKKLGLPD-TVSAIGILTITPSEASIIACDIATKSGAVEIGFLDRFT 79
Cdd:COG4810     1 MMDEEEKQRIIQEYVPGKQVTLAHIIANPDPDLYEKLGLDDeEAGAIGILTITPSEAAIIAADIATKAADVEIGFLDRFS 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1632924774  80 GAVVLTGDVSAIEYALSQVTRTLGEMMRFTTCPITRT 116
Cdd:COG4810    81 GSLVITGDVSSVESALREVVEYLGNVLGFTVCEITRT 117
 
Name Accession Description Interval E-value
EutS COG4810
Ethanolamine utilization protein EutS, microcompartment shell protein [Amino acid transport ...
 1-116 2.74e-66

Ethanolamine utilization protein EutS, microcompartment shell protein [Amino acid transport and metabolism];


Pssm-ID: 443838  Cd Length: 117  Bit Score: 195.46  E-value: 2.74e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632924774   1 MTTQHTTERMIQEYVPGKQVTLAHVIANPGKDLFKKLGLPD-TVSAIGILTITPSEASIIACDIATKSGAVEIGFLDRFT 79
Cdd:COG4810     1 MMDEEEKQRIIQEYVPGKQVTLAHIIANPDPDLYEKLGLDDeEAGAIGILTITPSEAAIIAADIATKAADVEIGFLDRFS 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1632924774  80 GAVVLTGDVSAIEYALSQVTRTLGEMMRFTTCPITRT 116
Cdd:COG4810    81 GSLVITGDVSSVESALREVVEYLGNVLGFTVCEITRT 117
BMC_PduU-EutS cd07046
1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), ...
 8-116 2.44e-62

1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain; PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to block the central pore that is present in other BMC domain proteins. EutS proteins included in this CD are sequence homologs of PduU. They are encoded within eut operon and may be required for the formation of the outer shell of bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutS might also form hexamers and play similar functional roles in the construction of the eut organelle outer shell at present no experimental evidence directly supports this view.


Pssm-ID: 132886  Cd Length: 110  Bit Score: 185.15  E-value: 2.44e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632924774   8 ERMIQEYVPGKQVTLAHVIANPGKDLFKKLGLPDTV-SAIGILTITPSEASIIACDIATKSGAVEIGFLDRFTGAVVLTG 86
Cdd:cd07046     1 QRIIQEYVPGKQITLAHLIANPDPEIYQKLGLNPGVdEAIGILTITPSEAAIIAADIATKAADVEIGFLDRFSGALVITG 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1632924774  87 DVSAIEYALSQVTRTLGEMMRFTTCPITRT 116
Cdd:cd07046    81 DVSEVESALEAVVDYLRETLGFTVCPITKT 110
PRK15468 PRK15468
ethanolamine utilization microcompartment protein EutS;
8-116 1.67e-37

ethanolamine utilization microcompartment protein EutS;


Pssm-ID: 185365  Cd Length: 111  Bit Score: 122.80  E-value: 1.67e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632924774   8 ERMIQEYVPGKQVTLAHVIANPGKDLFKKLGLPDTvSAIGILTITPSEASIIACDIATKSGAVEIGFLDRFTGAVVLTGD 87
Cdd:PRK15468    4 ERIIQEFVPGKQVTLAHLIAHPGEELAKKIGVPDA-GAIGIMTLTPGETAMIAGDLALKAADVHIGFLDRFSGALVIYGS 82

                          90       100
                  ....*....|....*....|....*....
gi 1632924774  88 VSAIEYALSQVTRTLGEMMRFTTCPITRT 116
Cdd:PRK15468   83 VGAVEEALSQTVSGLGRLLNYTLCEMTKS 111
BMC smart00877
Bacterial microcompartments are primitive organelles composed entirely of protein subunits; ...
 45-115 2.51e-13

Bacterial microcompartments are primitive organelles composed entirely of protein subunits; The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 197945  Cd Length: 75  Bit Score: 59.89  E-value: 2.51e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1632924774   45 AIGILTITPSEASIIACDIATKSGAVEIGFLDRFTG---AVVLTGDVSAIEYALSQVTRTLGEMMRFTTCPITR 115
Cdd:smart00877   1 ALGIIETRGAAAAIEAADAALKAANVELVGYESIGGgkvTVIITGDVAAVRAAVEAGLEAAERLGLVSSHVIPR 74
BMC pfam00936
BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein ...
 45-95 1.35e-10

BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 425954 [Multi-domain]  Cd Length: 74  Bit Score: 52.84  E-value: 1.35e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1632924774  45 AIGILTITPSEASIIACDIATKSGAVEIGFLDRFTGA---VVLTGDVSAIEYAL 95
Cdd:pfam00936   1 ALGLIETRGLAAGIEAADAMLKAANVELVGYELIGGGkvtVIITGDVAAVKAAV 54
 
Name Accession Description Interval E-value
EutS COG4810
Ethanolamine utilization protein EutS, microcompartment shell protein [Amino acid transport ...
 1-116 2.74e-66

Ethanolamine utilization protein EutS, microcompartment shell protein [Amino acid transport and metabolism];


Pssm-ID: 443838  Cd Length: 117  Bit Score: 195.46  E-value: 2.74e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632924774   1 MTTQHTTERMIQEYVPGKQVTLAHVIANPGKDLFKKLGLPD-TVSAIGILTITPSEASIIACDIATKSGAVEIGFLDRFT 79
Cdd:COG4810     1 MMDEEEKQRIIQEYVPGKQVTLAHIIANPDPDLYEKLGLDDeEAGAIGILTITPSEAAIIAADIATKAADVEIGFLDRFS 80

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1632924774  80 GAVVLTGDVSAIEYALSQVTRTLGEMMRFTTCPITRT 116
Cdd:COG4810    81 GSLVITGDVSSVESALREVVEYLGNVLGFTVCEITRT 117
BMC_PduU-EutS cd07046
1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), ...
 8-116 2.44e-62

1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain; PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to block the central pore that is present in other BMC domain proteins. EutS proteins included in this CD are sequence homologs of PduU. They are encoded within eut operon and may be required for the formation of the outer shell of bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutS might also form hexamers and play similar functional roles in the construction of the eut organelle outer shell at present no experimental evidence directly supports this view.


Pssm-ID: 132886  Cd Length: 110  Bit Score: 185.15  E-value: 2.44e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632924774   8 ERMIQEYVPGKQVTLAHVIANPGKDLFKKLGLPDTV-SAIGILTITPSEASIIACDIATKSGAVEIGFLDRFTGAVVLTG 86
Cdd:cd07046     1 QRIIQEYVPGKQITLAHLIANPDPEIYQKLGLNPGVdEAIGILTITPSEAAIIAADIATKAADVEIGFLDRFSGALVITG 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1632924774  87 DVSAIEYALSQVTRTLGEMMRFTTCPITRT 116
Cdd:cd07046    81 DVSEVESALEAVVDYLRETLGFTVCPITKT 110
PRK15468 PRK15468
ethanolamine utilization microcompartment protein EutS;
8-116 1.67e-37

ethanolamine utilization microcompartment protein EutS;


Pssm-ID: 185365  Cd Length: 111  Bit Score: 122.80  E-value: 1.67e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632924774   8 ERMIQEYVPGKQVTLAHVIANPGKDLFKKLGLPDTvSAIGILTITPSEASIIACDIATKSGAVEIGFLDRFTGAVVLTGD 87
Cdd:PRK15468    4 ERIIQEFVPGKQVTLAHLIAHPGEELAKKIGVPDA-GAIGIMTLTPGETAMIAGDLALKAADVHIGFLDRFSGALVIYGS 82

                          90       100
                  ....*....|....*....|....*....
gi 1632924774  88 VSAIEYALSQVTRTLGEMMRFTTCPITRT 116
Cdd:PRK15468   83 VGAVEEALSQTVSGLGRLLNYTLCEMTKS 111
BMC smart00877
Bacterial microcompartments are primitive organelles composed entirely of protein subunits; ...
 45-115 2.51e-13

Bacterial microcompartments are primitive organelles composed entirely of protein subunits; The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 197945  Cd Length: 75  Bit Score: 59.89  E-value: 2.51e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1632924774   45 AIGILTITPSEASIIACDIATKSGAVEIGFLDRFTG---AVVLTGDVSAIEYALSQVTRTLGEMMRFTTCPITR 115
Cdd:smart00877   1 ALGIIETRGAAAAIEAADAALKAANVELVGYESIGGgkvTVIITGDVAAVRAAVEAGLEAAERLGLVSSHVIPR 74
BMC cd06169
Bacterial Micro-Compartment (BMC) domain; Bacterial micro-compartments are primitive ...
 45-102 1.28e-12

Bacterial Micro-Compartment (BMC) domain; Bacterial micro-compartments are primitive protein-based organelles that sequester specific metabolic pathways in bacterial cells. The prototypical bacterial microcompartment is the carboxysome shell, a bacterial polyhedral organelle which increase the efficiency of CO2 fixation by encapsulating RuBisCO and carbonic anhydrase. They can be divided into two types: alpha-type carboxysomes (alpha-cyanobacteria and proteobacteria) and beta-type carboxysomes (beta-cyanobacteria). In addition to these proteins there are several homologous shell proteins including those found in pdu organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol and eut organelles involved in the cobalamin-dependent degradation of ethanolamine. Structure evidence shows that several carboxysome shell proteins and their homologs (Csos1A, CcmK1,2,4, and PduU) exist as hexamers which might further assemble into extended, tightly packed layers hypothesized to represent the flat facets of the polyhedral organelles outer shell. Although it has been suggested that other homologous proteins in this family might also form hexamers and play similar functional roles in the construction of their corresponding organelle outer shell at present no experimental evidence directly supports this view.


Pssm-ID: 132884  Cd Length: 62  Bit Score: 58.04  E-value: 1.28e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1632924774  45 AIGILTITPSEASIIACDIATKSGAVEIGFLDRF----TGAVVLTGDVSAIEYALSQVTRTL 102
Cdd:cd06169     1 ALGLLEVRGLAAAIVAADAAVKAADVELVGIERAggggLVTLIIRGDVSAVKAAVEAAEQAA 62
BMC pfam00936
BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein ...
 45-95 1.35e-10

BMC domain; Bacterial microcompartments are primitive organelles composed entirely of protein subunits. The prototypical bacterial microcompartment is the carboxysome, a protein shell for sequestering carbon fixation reactions. These proteins for hexameric structure.


Pssm-ID: 425954 [Multi-domain]  Cd Length: 74  Bit Score: 52.84  E-value: 1.35e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1632924774  45 AIGILTITPSEASIIACDIATKSGAVEIGFLDRFTGA---VVLTGDVSAIEYAL 95
Cdd:pfam00936   1 ALGLIETRGLAAGIEAADAMLKAANVELVGYELIGGGkvtVIITGDVAAVKAAV 54
BMC_EutL_repeat1 cd07049
ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1; ...
 20-72 1.85e-06

ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1; EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).


Pssm-ID: 132889  Cd Length: 103  Bit Score: 43.17  E-value: 1.85e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1632924774  20 VTLAHVIANPGKDLFKKLGLPDTVSAIGILTITPSEASIIACDIATKSGAVEI 72
Cdd:cd07049     1 VLAVKVIPNVDPDLAKELSLPPHHRSLGIITADSDDVTYTALDEATKAAEVEV 53
PRK15405 PRK15405
ethanolamine utilization microcompartment protein EutL;
19-72 1.95e-05

ethanolamine utilization microcompartment protein EutL;


Pssm-ID: 185303 [Multi-domain]  Cd Length: 217  Bit Score: 41.60  E-value: 1.95e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1632924774  19 QVTLAHVIANPGKDLFKKLGLPDTVSAIGILTITPSEASIIACDIATKSGAVEI 72
Cdd:PRK15405    9 SVLAMRVIANVNAGLARELKLPPHIRSLGLITADSDDVTYTALDEATKQAMVEV 62
BMC_PduT_repeat2 cd07054
1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat ...
 45-104 5.72e-05

1,2-propanediol utilization protein T (PduT), Bacterial Micro-Compartment (BMC) domain repeat 2; PduT proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles which are involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduT might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles, at present no experimental evidence directly supports this view. PduT proteins contain two tandem BMC domains repeats. This CD contains repeat 2 (the second BMC domain of PduT) as well as carboxysome shell protein sequence homolog, EutM protein, are also included in this CD. They too might exist as hexamers and might play similar functional roles in the construction of the eut organelle outer shell which still remains poorly understood.


Pssm-ID: 132894  Cd Length: 78  Bit Score: 38.69  E-value: 5.72e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1632924774  45 AIGILTITPSEASIIACDIATKSGAVEIG--FLDRFTGA---VVLTGDVSAIEYALSQVTRTLGE 104
Cdd:cd07054     1 ALGVIETFSVASGIVAADAALKAADVQLIeiRLAMGIGGksfVVLTGDVSAVEAAVEAAEAVVGE 65
EutL COG4816
Ethanolamine utilization protein EutL, microcompartment shell protein [Amino acid transport ...
 18-72 8.97e-05

Ethanolamine utilization protein EutL, microcompartment shell protein [Amino acid transport and metabolism];


Pssm-ID: 443844 [Multi-domain]  Cd Length: 216  Bit Score: 39.85  E-value: 8.97e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1632924774  18 KQVTLAHVIANPGKDLFKKLGLPDTVSAIGILTITPSEASIIACDIATKSGAVEI 72
Cdd:COG4816     7 AKVLAEVVIANVDPDLAEKLGLDPKYRSIGIITADTDDVPYIAADEATKAANVEV 61
PRK15415 PRK15415
propanediol utilization microcompartment protein PduB;
21-104 5.96e-04

propanediol utilization microcompartment protein PduB;


Pssm-ID: 185313 [Multi-domain]  Cd Length: 266  Bit Score: 37.78  E-value: 5.96e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1632924774  21 TLAHVIANPGKDLFKKLGLPDTVSAIGIL-TITPSEASIIACDIATKSGAVEIGF--LDRFT------GAVVLTG--DVS 89
Cdd:PRK15415   52 TIGLVIANVDSALLEAMKLEKKYRSIGILgARTGAGPQIMAADEAVKATNTEVVSieLPRDTkggaghGSLIIFGaeDVS 131

                          90
                  ....*....|....*....
gi 1632924774  90 ----AIEYALSQVTRTLGE 104
Cdd:PRK15415  132 dvrrAVEVALKELDRTFGD 150
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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