Reviewed, UniProtKB/Swiss-Prot Q9Z4Q7 (PRDB_CLOST)

Names and origin

Protein names

Recommended name:
    D-proline reductase subunit gamma
    EC=1.21.4.1
Alternative name(s):
    D-proline reductase 26 kDa subunit

Gene names

Name:

prdB

Organism

Clostridium sticklandii

Taxonomic identifier

1511 [NCBI]

Taxonomic lineage

Bacteria › Firmicutes › Clostridia › Clostridiales › Clostridiaceae › Clostridium

Protein attributes

Sequence length	242 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
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	This subunit is carbonylated in vitro on an unidentified residue.
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
Coding sequence diversity	Selenocysteine
Ligand	Selenium
Molecular function	Oxidoreductase
Technical term	Direct protein sequencing
Gene Ontology (GO)
Biological process	oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	glycine reductase complex Inferred from electronic annotation. Source: InterPro
Molecular function	D-proline reductase (dithiol) activity Inferred from electronic annotation. Source: EC glycine reductase activity Inferred from electronic annotation. Source: InterPro selenium binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 242	242	D-proline reductase subunit gamma		PRO_0000240012
Sites
	Active site	152	1	Nucleophile Probable
Amino acid modifications
	Non-standard residue	152	1	Selenocysteine

Sequences

	Sequence		Length	Mass (Da)
	Q9Z4Q7-1 [UniParc]. Last modified February 26, 2008. Version 3. Checksum: 529A941DA88229C5	FASTA	242	25,812
	10 20 30 40 50 60 MSDLTVVKGL QSEIYVPITP PPVWTPVTKE LKDMTVALVT AAGVHMKADK RFNLAGDFSF 70 80 90 100 110 120 RVIPGDASVN DMMVSHGGYD NGDVNKDINC MFPIDPMRTL AKEGFIKALA PINIGFMGGG 130 140 150 160 170 180 GDQKKFSEET GPEIARQLKE EGVDAVLLTA GUGTCHRSAV IVQRAIEESG IPTIIIAALP 190 200 210 220 230 240 PVVRQNGTPR AVAPLVPMGA NAGEPNNPEM QKAICTDSLK QLVEIPSAGK IVPLPYEYVA KV

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 1-19; 51-80; 87-102; 140-161 AND 231-242, SELENOCYSTEINE AT SEC-152, SUBUNIT, SUBCELLULAR LOCATION. Strain: ATCC 12662 / DSM 519 / JCM 1433 / NCIB 10654.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AJ130879 Genomic DNA. Translation: CAB38127.2.
3D structure databases
ModBase	Search...
Enzyme and pathway databases
BioCyc	MetaCyc:PRDBST-MON.
BRENDA	1.21.4.1. 1159.
Family and domain databases
InterPro	IPR010187. Various_sel_PB. [Graphical view]
Pfam	PF07355. GRDB. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

PRDB_CLOST

Accession

Primary (citable) accession number: Q9Z4Q7

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 13, 2006
Last sequence update:	February 26, 2008
Last modified:	January 20, 2009
This is version 35 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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