PDUA_CITFR
ID PDUA_CITFR Reviewed; 93 AA.
AC P0DUM6;
DT 25-MAY-2022, integrated into UniProtKB/Swiss-Prot.
DT 25-MAY-2022, sequence version 1.
DT 03-AUG-2022, entry version 2.
DE RecName: Full=Bacterial microcompartment shell protein PduA {ECO:0000303|PubMed:18332146};
DE AltName: Full=Bacterial microcompartment protein homohexamer {ECO:0000305};
DE Short=BMC-H {ECO:0000305};
DE AltName: Full=Propanediol utilization protein PduA;
GN Name=pduA {ECO:0000303|PubMed:18332146};
OS Citrobacter freundii.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Citrobacter; Citrobacter freundii complex.
OX NCBI_TaxID=546;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, IDENTIFICATION BY MASS
RP SPECTROMETRY, PATHWAY, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=18332146; DOI=10.1074/jbc.m709214200;
RA Parsons J.B., Dinesh S.D., Deery E., Leech H.K., Brindley A.A., Heldt D.,
RA Frank S., Smales C.M., Lunsdorf H., Rambach A., Gass M.H., Bleloch A.,
RA McClean K.J., Munro A.W., Rigby S.E.J., Warren M.J., Prentice M.B.;
RT "Biochemical and Structural Insights into Bacterial Organelle Form and
RT Biogenesis.";
RL J. Biol. Chem. 283:14366-14375(2008).
RN [2]
RP FUNCTION, INTERACTION WITH PDUB; PDUB'; PDUJ; PDUK; PDUN AND PDUU, SUBUNIT,
RP SUBCELLULAR LOCATION, BIOTECHNOLOGY (ARTIFICIAL BMCS), AND MUTAGENESIS OF
RP SER-93.
RX PubMed=20417607; DOI=10.1016/j.molcel.2010.04.008;
RA Parsons J.B., Frank S., Bhella D., Liang M., Prentice M.B., Mulvihill D.P.,
RA Warren M.J.;
RT "Synthesis of empty bacterial microcompartments, directed organelle protein
RT incorporation, and evidence of filament-associated organelle movement.";
RL Mol. Cell 38:305-315(2010).
RN [3]
RP BIOTECHNOLOGY (ARTIFICIAL BMCS).
RX PubMed=24933391; DOI=10.1021/sb4001118;
RA Lawrence A.D., Frank S., Newnham S., Lee M.J., Brown I.R., Xue W.F.,
RA Rowe M.L., Mulvihill D.P., Prentice M.B., Howard M.J., Warren M.J.;
RT "Solution structure of a bacterial microcompartment targeting peptide and
RT its application in the construction of an ethanol bioreactor.";
RL ACS Synth. Biol. 3:454-465(2014).
RN [4]
RP MODELING OF BMCS, FUNCTION, SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=25646976; DOI=10.1371/journal.pcbi.1004067;
RA Jorda J., Liu Y., Bobik T.A., Yeates T.O.;
RT "Exploring bacterial organelle interactomes: a model of the protein-protein
RT interaction network in the Pdu microcompartment.";
RL PLoS Comput. Biol. 11:e1004067-e1004067(2015).
RN [5]
RP BIOTECHNOLOGY (INTRACELLULAR SCAFFOLDS).
RX PubMed=29227472; DOI=10.1038/nchembio.2535;
RA Lee M.J., Mantell J., Hodgson L., Alibhai D., Fletcher J.M., Brown I.R.,
RA Frank S., Xue W.F., Verkade P., Woolfson D.N., Warren M.J.;
RT "Engineered synthetic scaffolds for organizing proteins within the
RT bacterial cytoplasm.";
RL Nat. Chem. Biol. 14:142-147(2018).
RN [6]
RP FUNCTION, DISRUPTION PHENOTYPE, AND BIOTECHNOLOGY (PERMUTATED PROTEIN).
RX PubMed=29573556; DOI=10.1002/smll.201704020;
RA Uddin I., Frank S., Warren M.J., Pickersgill R.W.;
RT "A Generic Self-Assembly Process in Microcompartments and Synthetic Protein
RT Nanotubes.";
RL Small 14:e1704020-e1704020(2018).
RN [7] {ECO:0007744|PDB:4P7T, ECO:0007744|PDB:4P7V}
RP X-RAY CRYSTALLOGRAPHY (1.72 ANGSTROMS) OF MUTATED 1-92, FUNCTION, SUBUNIT,
RP AND MUTAGENESIS OF LYS-26; VAL-51; ARG-79 AND SER-93.
RX PubMed=24873823; DOI=10.1074/jbc.m114.569285;
RA Pang A., Frank S., Brown I., Warren M.J., Pickersgill R.W.;
RT "Structural insights into higher order assembly and function of the
RT bacterial microcompartment protein PduA.";
RL J. Biol. Chem. 289:22377-22384(2014).
CC -!- FUNCTION: One of the major shell proteins of the bacterial
CC microcompartment (BMC) dedicated to 1,2-propanediol (1,2-PD)
CC degradation, probably important for metabolite diffusion into and out
CC of the BMC (Probable). Overexpression of a C-terminally mutated form
CC (PduA*) makes thin parallel filaments with a honeycomb-like assembly in
CC cross-section that probably form nanotubes. The filaments interfere
CC with septation (PubMed:20417607, PubMed:24873823, PubMed:29227472).
CC PduA is probably the hub for binding multiple enzymes to the interior
CC of the BMC (Probable). At least one of PduA or PduJ is required for BMC
CC assembly; it must be encoded as the first gene in the pdu operon (By
CC similarity). {ECO:0000250|UniProtKB:P37448,
CC ECO:0000269|PubMed:20417607, ECO:0000269|PubMed:24873823,
CC ECO:0000269|PubMed:29227472, ECO:0000305|PubMed:20417607,
CC ECO:0000305|PubMed:24873823, ECO:0000305|PubMed:25646976,
CC ECO:0000305|PubMed:29573556}.
CC -!- FUNCTION: Expression of a cosmid containing the full 21-gene pdu operon
CC in E.coli allows E.coli to grow on 1,2-PD with the appearance of BMCs
CC in its cytoplasm. Overexpression of this protein leads to aberrant
CC intracellular filaments. {ECO:0000269|PubMed:18332146}.
CC -!- FUNCTION: The 1,2-PD-specific bacterial microcompartment (BMC)
CC concentrates low levels of 1,2-PD catabolic enzymes, concentrates
CC volatile reaction intermediates thus enhancing pathway flux and keeps
CC the level of toxic, mutagenic propionaldehyde low.
CC {ECO:0000305|PubMed:20417607}.
CC -!- PATHWAY: Polyol metabolism; 1,2-propanediol degradation.
CC {ECO:0000269|PubMed:18332146}.
CC -!- SUBUNIT: Homohexamer with a central pore; Lys-26 and Arg-79
CC interactions are very important for hexamer symmetry (PubMed:24873823).
CC The hexamers pack against each other in arrays (By similarity).
CC Interacts individually with shell proteins PduB, PduB', PduJ, PduK,
CC PduN and PduU (PubMed:20417607). Modeling suggests PduC, PduD, PduE,
CC PduL and PduP interact with a cleft formed by the C-terminal segments
CC of 2 adjacent PduA subunits (on the BMC luminal side) in the hexamer
CC (Probable). {ECO:0000250|UniProtKB:P0A1C7, ECO:0000269|PubMed:20417607,
CC ECO:0000269|PubMed:24873823, ECO:0000305|PubMed:25646976}.
CC -!- SUBCELLULAR LOCATION: Bacterial microcompartment
CC {ECO:0000269|PubMed:18332146, ECO:0000269|PubMed:20417607}. Note=In
CC BMCs the hexamer concave side probably faces outward, with the N- and
CC C-termini exposed to the cytoplasm (Probable). Modeling suggests the
CC concave face (with both termini) is in the interior of the BMC
CC (Probable). {ECO:0000305|PubMed:25646976, ECO:0000305|PubMed:29227472}.
CC -!- DISRUPTION PHENOTYPE: When the whole pdu operon except this gene is
CC expressed in E.coli no BMCs are made; with the whole operon many BMCs
CC are produced in E.coli (PubMed:18332146). This gene is not essential
CC for BMC formation; a pduB/B'-pduJ-pduK-pduN-pduU-pduT strain produces
CC BMCs in E.coli (PubMed:29573556). {ECO:0000269|PubMed:18332146,
CC ECO:0000269|PubMed:29573556}.
CC -!- BIOTECHNOLOGY: Artificial BMCs can be made in E.coli by expressing
CC pduA-pduB/B'-pduJ-pduK-pduN-pduU-pduT (in this order); pduT and pduU
CC are optional, while pduA, pduB/B', pduJ, pduK and pduN are essential. A
CC construct with the reversed gene order does not make BMCs
CC (PubMed:20417607). Ethanogenic BMCs can be made in E.coli by targeting
CC pyruvate decarboxylase (pdc) and alcohol dehydrogenase (adh) to them.
CC PduP(1-18)-Pdc and PduD(1-18)-Adh strains targeted to the BMC (PduA,
CC PduB, PduJ, PduK, PduN, PduU) make significantly more ethanol than
CC strains where Pdc and Adh are not targeted to the BMC
CC (PubMed:24933391). A circularly permutated form can be made in which
CC residues 69-89 are displaced to the beginning of the protein with an
CC extra linker. Both termini of this construct are probably in the BMC
CC lumen and it can be used to target proteins to the BMC interior
CC (PubMed:29573556). {ECO:0000269|PubMed:20417607,
CC ECO:0000269|PubMed:24933391, ECO:0000269|PubMed:29573556}.
CC -!- BIOTECHNOLOGY: Can be used to make a synthetic intracellular scaffold
CC that fills the E.coli cytoplasm by adding a heterodimeric coiled-coil
CC system (CC-Di-AB). PduA* is N-terminally tagged with CC-Di-B which
CC makes the scaffold, while other proteins can be targeted to the
CC scaffold using a CC-Di-A tag. A strain that produces increased amounts
CC of ethanol (using pdc and adh) has been made as proof of concept. The
CC scaffolds can also be targeted to the cell inner membrane
CC (PubMed:29227472). The same CC-Di-B construct also targets proteins to
CC the BMC, probably on the exterior face (PubMed:29573556).
CC {ECO:0000269|PubMed:29227472, ECO:0000269|PubMed:29573556}.
CC -!- SIMILARITY: Belongs to the bacterial microcompartments protein family.
CC {ECO:0000255|PROSITE-ProRule:PRU01278}.
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DR EMBL; AM498294; CAM57283.1; -; Genomic_DNA.
DR PDB; 4P7T; X-ray; 1.72 A; A/B/C/D/E/F=1-92.
DR PDB; 4P7V; X-ray; 1.93 A; A/B/C/D/E/F=1-92.
DR PDBsum; 4P7T; -.
DR PDBsum; 4P7V; -.
DR UniPathway; UPA00621; -.
DR GO; GO:0031469; C:bacterial microcompartment; IEA:UniProtKB-SubCell.
DR GO; GO:0051144; P:propanediol catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.30.70.1710; -; 1.
DR InterPro; IPR020808; Bact_microcomp_CS.
DR InterPro; IPR000249; BMC_dom.
DR InterPro; IPR037233; CcmK-like_sf.
DR InterPro; IPR044872; CcmK/CsoS1_BMC.
DR Pfam; PF00936; BMC; 1.
DR SMART; SM00877; BMC; 1.
DR SUPFAM; SSF143414; SSF143414; 1.
DR PROSITE; PS01139; BMC_1; 1.
DR PROSITE; PS51930; BMC_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Bacterial microcompartment; Transport.
FT CHAIN 1..93
FT /note="Bacterial microcompartment shell protein PduA"
FT /id="PRO_0000454246"
FT DOMAIN 5..89
FT /note="BMC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01278"
FT MUTAGEN 26
FT /note="K->A: Forms sheets but not nanotubes upon
FT overexpression of PduA*."
FT /evidence="ECO:0000269|PubMed:24873823"
FT MUTAGEN 26
FT /note="K->D: No intracellular structures formed upon
FT overexpression of PduA*, decreases stability of hexamers
FT which are no longer symmetric and do not form arrays
FT correctly."
FT /evidence="ECO:0000269|PubMed:24873823"
FT MUTAGEN 51
FT /note="V->A: Forms sheets and altered nanotubes upon
FT overexpression of PduA*."
FT /evidence="ECO:0000269|PubMed:24873823"
FT MUTAGEN 51
FT /note="V->D: No structures formed upon overexpression of
FT PduA*."
FT /evidence="ECO:0000269|PubMed:24873823"
FT MUTAGEN 79
FT /note="R->A: Forms sheets but not nanotubes upon
FT overexpression of PduA*."
FT /evidence="ECO:0000269|PubMed:24873823"
FT MUTAGEN 93
FT /note="S->RLVKDPAANKARKEAELAAATAEQ: PduA*, a soluble form
FT used for crystal structure determination."
FT /evidence="ECO:0000269|PubMed:20417607,
FT ECO:0000269|PubMed:24873823, ECO:0007744|PDB:4P7T,
FT ECO:0007744|PDB:4P7V"
SQ SEQUENCE 93 AA; 9464 MW; CC7C793F19DE1E36 CRC64;
MQQEALGMVE TKGLTAAIEA ADAMVKSANV MLVGYEKIGS GLVTVIVRGD VGAVKAATDA
GAAAARNVGE VKAVHVIPRP HTDVEKILPK GIS
