Reviewed, UniProtKB/Swiss-Prot Q9Z4P6 (PRDA_CLOST)

Names and origin

Protein names

Recommended name:
    D-proline reductase proprotein prdA
    EC=1.21.4.1
Cleaved into the following 2 chains:
    1- Recommended name:
            D-proline reductase subunit beta
        Alternative name(s):
            D-proline reductase 45 kDa subunit
    2- Recommended name:
            D-proline reductase subunit alpha
        Alternative name(s):
            D-proline reductase 23 kDa subunit

Gene names

Name:

prdA

Organism

Clostridium sticklandii

Taxonomic identifier

1511 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium

Protein attributes

Sequence length	630 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	D-proline reductase catalyzes the reductive cleavage of a C-N bond in D-proline resulting in the formation of 5-aminovalerate. The alpha subunit has been shown to bind D-proline, presumably via the pyruvoyl group.
Catalytic activity	5-aminopentanoate + lipoate = D-proline + dihydrolipoate.
Subunit structure	Consists of 3 subunits of 23, 26 and 45 kDa (alpha, gamma and beta respectively). The molecular weight of the complex is approximately 870 kDa, suggesting a decameric structure, if all 3 subunits are present in equal stoichiometry. Ref.1
Subcellular location	Cytoplasm. Ref.1
Post-translational modification	The peptide chain is cleaved into beta and alpha chains, and the alpha chain N-terminal cysteine is deaminated and oxidized to form a reactive pyruvoyl group By similarity.
Miscellaneous	The reaction mechanism first involves the formation of an adduct (and not a Schiff base) between the nitrogen of proline and the pyruvoyl group of the alpha subunit. The selenol anion of selenocysteine in prdB nucleophilically attacks the alpha-carbon, resulting in cleavage of the N-C bond of the proline ring. This intermediate is then transformed to the oxidized gamma subunit containing a mixed selenide/sulfide group and to the 5-aminovalerate adduct of the alpha subunit. The final product, 5-aminovalerate, is formed by hydrolysis. Subsequently, the selenide-sulfide group of prdB is reduced, but the natural electron donating system for D-proline reductase is unknown.

Ontologies

Keywords
Cellular component	Cytoplasm
Ligand	Pyruvate
Molecular function	Oxidoreductase
Technical term	Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	D-proline reductase (dithiol) activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 425	425	D-proline reductase subunit beta		PRO_0000240010
	Chain	426 – 630	205	D-proline reductase subunit alpha		PRO_0000240011
Sites
	Active site	426	1	Covalent intermediate with substrate; via pyruvic acid Probable
Amino acid modifications
	Modified residue	426	1	Pyruvic acid (Cys) Probable

Sequences

	Sequence		Length	Mass (Da)
	Q9Z4P6-1 [UniParc]. Last modified May 1, 1999. Version 1. Checksum: 8C757A5C01AF9FDA	FASTA	630	67,713
	10 20 30 40 50 60 MSITLESAKE HANDLAVLCC RAEEGTVIGP SNLEDPAIFG DLEDSGLLTI PANCLKIGEV 70 80 90 100 110 120 LGAKLVKTAD SLTPLTPELL EGVNSISEEA PKQEASAPVE APVAEVAPAA MPVANVTGSM 130 140 150 160 170 180 LKIHIGEGKD INLEIPLTIA GQMGVVAPTA AAPAGVAMPV ASATEQVVAP AGEPKLVRTL 190 200 210 220 230 240 QKKHFQNLRK VEFGPETKIE NNTIYIRENI CEDAVKVSNL VTDIKVEIIT PADYGKYSET 250 260 270 280 290 300 IMDVQPIATK EGDGKIGQGV TRVIDGAIIM VTGTDEDGVQ IGEFGSSEGE LDANIMWGRP 310 320 330 340 350 360 GAPDKGEILI KTQVTIKAGT NMERPGPLAA HKATDFITQE IREALKKLDD SEVVETEELA 370 380 390 400 410 420 QYRRPGKKKV VIIKEIMGQG AMHDNLILPV EPVGVIGAKP NVDLGNVPVV LSPLEVLDGG 430 440 450 460 470 480 IHALTCIGPA SKENSRHYWR EPLVIEVMND EEFDLAGVVF VGSPQVNAEK FYVSERLGML 490 500 510 520 530 540 VETMDVEGAF ITTEGFGNNH IDFASHHEQV GMRGIPVVGM SFCAVQGALV VGNKYMKYMV 550 560 570 580 590 600 DNNKSEQGIE NEILSNNTLC PEDAIRAVAM LKAAIAEEEV KVAERKFSKN VKENNVDLIE 610 620 630 EQAGKEITLL PNEQVLPMSK REKEIYEADK

References

[1]

"Identification of D-proline reductase from Clostridium sticklandii as a selenoenzyme and indications for a catalytically active pyruvoyl group derived from a cysteine residue by cleavage of a proprotein." Kabisch U.C., Graentzdoerffer A., Schierhorn A., Ruecknagel K.P., Andreesen J.R., Pich A. J. Biol. Chem. 274:8445-8454(1999) [PubMed: 10085076] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-18; 191-225; 256-304; 400-425; 427-456; 471-491; 545-564; 573-581 AND 593-605, SUBUNIT, SUBCELLULAR LOCATION, CHARACTERIZATION. Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654.

[2]

"In vitro processing of the proproteins grdE of protein B of glycine reductase and prdA of D-proline reductase from Clostridium sticklandii: formation of a pyruvoyl group from a cysteine residue." Bednarski B., Andreesen J.R., Pich A. Eur. J. Biochem. 268:3538-3544(2001) [PubMed: 11422384] [Abstract] Cited for: PROTEOLYTIC PROCESSING IN VITRO.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AJ130879 Genomic DNA. Translation: CAB38126.1.
3D structure databases
ModBase	Search...
Enzyme and pathway databases
BioCyc	MetaCyc:PRDAST-MON.
BRENDA	1.21.4.1. 1159.
Family and domain databases
ProtoNet	Search...

Entry information

Entry name

PRDA_CLOST

Accession

Primary (citable) accession number: Q9Z4P6

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 13, 2006
Last sequence update:	May 1, 1999
Last modified:	June 16, 2009
This is version 29 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)