PRDA_ACESD
ID PRDA_ACESD Reviewed; 629 AA.
AC Q9Z4P6; E3PTZ9;
DT 13-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 08-FEB-2011, sequence version 2.
DT 03-AUG-2022, entry version 80.
DE RecName: Full=D-proline reductase proprotein PrdA;
DE EC=1.21.4.1 {ECO:0000269|PubMed:10085076};
DE Contains:
DE RecName: Full=D-proline reductase subunit beta;
DE AltName: Full=D-proline reductase 45 kDa subunit;
DE Contains:
DE RecName: Full=D-proline reductase subunit alpha;
DE AltName: Full=D-proline reductase 23 kDa subunit;
GN Name=prdA; OrderedLocusNames=CLOST_2234;
OS Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG
OS 9281 / NCIMB 10654 / HF) (Clostridium sticklandii).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Peptostreptococcaceae;
OC Acetoanaerobium.
OX NCBI_TaxID=499177;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-18; 190-224;
RP 255-303; 399-424; 426-455; 470-490; 544-563; 572-580 AND 592-604, SUBUNIT,
RP SUBCELLULAR LOCATION, FUNCTION, CATALYTIC ACTIVITY, AND CHARACTERIZATION.
RC STRAIN=ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF;
RX PubMed=10085076; DOI=10.1074/jbc.274.13.8445;
RA Kabisch U.C., Graentzdoerffer A., Schierhorn A., Ruecknagel K.P.,
RA Andreesen J.R., Pich A.;
RT "Identification of D-proline reductase from Clostridium sticklandii as a
RT selenoenzyme and indications for a catalytically active pyruvoyl group
RT derived from a cysteine residue by cleavage of a proprotein.";
RL J. Biol. Chem. 274:8445-8454(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF;
RX PubMed=20937090; DOI=10.1186/1471-2164-11-555;
RA Fonknechten N., Chaussonnerie S., Tricot S., Lajus A., Andreesen J.R.,
RA Perchat N., Pelletier E., Gouyvenoux M., Barbe V., Salanoubat M.,
RA Le Paslier D., Weissenbach J., Cohen G.N., Kreimeyer A.;
RT "Clostridium sticklandii, a specialist in amino acid degradation:revisiting
RT its metabolism through its genome sequence.";
RL BMC Genomics 11:555-555(2010).
RN [3]
RP PROTEOLYTIC PROCESSING IN VITRO.
RC STRAIN=ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF;
RX PubMed=11422384; DOI=10.1046/j.1432-1327.2001.02257.x;
RA Bednarski B., Andreesen J.R., Pich A.;
RT "In vitro processing of the proproteins grdE of protein B of glycine
RT reductase and prdA of D-proline reductase from Clostridium sticklandii:
RT formation of a pyruvoyl group from a cysteine residue.";
RL Eur. J. Biochem. 268:3538-3544(2001).
CC -!- FUNCTION: D-proline reductase catalyzes the reductive cleavage of a C-N
CC bond in D-proline resulting in the formation of 5-aminovalerate. The
CC alpha subunit has been shown to bind D-proline, presumably via the
CC pyruvoyl group. {ECO:0000269|PubMed:10085076}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5-aminopentanoate + [PrdC protein]-Se-L-selenocysteinyl-S-L-
CC cysteine = [PrdC protein]-L-selenocysteine/L-cysteine + D-proline;
CC Xref=Rhea:RHEA:12737, Rhea:RHEA-COMP:14983, Rhea:RHEA-COMP:14984,
CC ChEBI:CHEBI:29950, ChEBI:CHEBI:30000, ChEBI:CHEBI:57726,
CC ChEBI:CHEBI:142235, ChEBI:CHEBI:356010; EC=1.21.4.1;
CC Evidence={ECO:0000269|PubMed:10085076};
CC -!- SUBUNIT: Consists of 3 subunits of 23, 26 and 45 kDa (alpha, gamma and
CC beta respectively). The molecular weight of the complex is
CC approximately 870 kDa, suggesting a decameric structure, if all 3
CC subunits are present in equal stoichiometry.
CC {ECO:0000269|PubMed:10085076}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:10085076}.
CC -!- PTM: The peptide chain is cleaved into beta and alpha chains, and the
CC alpha chain N-terminal cysteine is deaminated and oxidized to form a
CC reactive pyruvoyl group. {ECO:0000250}.
CC -!- MISCELLANEOUS: The reaction mechanism first involves the formation of
CC an adduct (and not a Schiff base) between the nitrogen of proline and
CC the pyruvoyl group of the alpha subunit. The selenol anion of
CC selenocysteine in PrdB nucleophilically attacks the alpha-carbon,
CC resulting in cleavage of the N-C bond of the proline ring. This
CC intermediate is then transformed to the oxidized gamma subunit
CC containing a mixed selenide/sulfide group and to the 5-aminovalerate
CC adduct of the alpha subunit. The final product, 5-aminovalerate, is
CC formed by hydrolysis. Subsequently, the selenide-sulfide group of PrdB
CC is reduced, but the natural electron donating system for D-proline
CC reductase is unknown.
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DR EMBL; AJ130879; CAB38126.1; -; Genomic_DNA.
DR EMBL; FP565809; CBH22353.1; -; Genomic_DNA.
DR AlphaFoldDB; Q9Z4P6; -.
DR STRING; 1511.CLOST_2234; -.
DR PRIDE; Q9Z4P6; -.
DR EnsemblBacteria; CBH22353; CBH22353; CLOST_2234.
DR KEGG; cst:CLOST_2234; -.
DR eggNOG; COG0252; Bacteria.
DR eggNOG; COG5275; Bacteria.
DR HOGENOM; CLU_469055_0_0_9; -.
DR OMA; ENSRHYW; -.
DR BioCyc; MetaCyc:PRDAST-MON; -.
DR Proteomes; UP000007041; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0050002; F:D-proline reductase (dithiol) activity; IDA:CACAO.
DR InterPro; IPR031002; D_pro_red_PrdA.
DR InterPro; IPR015417; Gly_reductase_pB_sua/b.
DR Pfam; PF09338; Gly_reductase; 1.
DR TIGRFAMs; TIGR04480; D_pro_red_PrdA; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Direct protein sequencing; Oxidoreductase; Pyruvate;
KW Reference proteome.
FT CHAIN 1..424
FT /note="D-proline reductase subunit beta"
FT /id="PRO_0000240010"
FT CHAIN 425..629
FT /note="D-proline reductase subunit alpha"
FT /id="PRO_0000240011"
FT ACT_SITE 425
FT /note="Covalent intermediate with substrate; via pyruvic
FT acid"
FT /evidence="ECO:0000305"
FT MOD_RES 425
FT /note="Pyruvic acid (Cys)"
FT /evidence="ECO:0000305"
FT CONFLICT 186..188
FT /note="KIE -> QNLR (in Ref. 1; CAB38126)"
FT /evidence="ECO:0000305"
FT CONFLICT 587
FT /note="N -> S (in Ref. 1; CAB38126)"
FT /evidence="ECO:0000305"
FT CONFLICT 620..621
FT /note="KR -> RE (in Ref. 1; CAB38126)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 629 AA; 67598 MW; DC7EDFB0C879A197 CRC64;
MSITLESAKE HANDLAVLCC RAEEGTVIGP SNLEDPAIFG DLEDSGLLTI PANCLKIGEV
LGAKLVKTAD SLTPLTPELL EGVNSISEEA PKQEASAPVE APVAEVAPAA MPVANVTGSM
LKIHIGEGKD INLEIPLTIA GQMGVVAPTA AAPAGVAMPV ASATEQVVAP AGEPKLVRTL
QKKHFKIEKV EFGPETKIEN NTIYIRENIC EDAVKVSNLV TDIKVEIITP ADYGKYSETI
MDVQPIATKE GDGKIGQGVT RVIDGAIIMV TGTDEDGVQI GEFGSSEGEL DANIMWGRPG
APDKGEILIK TQVTIKAGTN MERPGPLAAH KATDFITQEI REALKKLDDS EVVETEELAQ
YRRPGKKKVV IIKEIMGQGA MHDNLILPVE PVGVIGAKPN VDLGNVPVVL SPLEVLDGGI
HALTCIGPAS KENSRHYWRE PLVIEVMNDE EFDLAGVVFV GSPQVNAEKF YVSERLGMLV
ETMDVEGAFI TTEGFGNNHI DFASHHEQVG MRGIPVVGMS FCAVQGALVV GNKYMKYMVD
NNKSEQGIEN EILSNNTLCP EDAIRAVAML KAAIAEEEVK VAERKFNKNV KENNVDLIEE
QAGKEITLLP NEQVLPMSKK RKEIYEADK
