P37426 (RIR1_SALTY) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Ribonucleoside-diphosphate reductase 1 subunit alpha
EC=1.17.4.1

Alternative name(s):
Protein B1
Ribonucleoside-diphosphate reductase 1 R1 subunit
Ribonucleotide reductase 1

Gene names

Name:	nrdA
Ordered Locus Names:	STM2277

Organism

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]

Taxonomic identifier

99287 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Salmonella › Salmonella choleraesuis › Salmonella enterica I › Salmonella typhimurium

Protein attributes

Sequence length	761 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides. R1 contains the binding sites for both substrates and allosteric effectors and carries out the actual reduction of the ribonucleotide.
Catalytic activity	2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.
Enzyme regulation	Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding to separate specificity and activation sites on the alpha subunit. The type of nucleotide bound at the specificity site determines substrate preference. It seems probable that ATP makes the enzyme reduce CDP and UDP, dGTP favors ADP reduction and dTTP favors GDP reduction. Stimulated by ATP and inhibited by dATP binding to the activity site By similarity.
Pathway	Genetic information processing; DNA replication.
Subunit structure	Tetramer of two alpha (R1) and two beta (R2) subunits. The B1 protein is a dimer of alpha subunits. A radical transfer pathway occurs between 'Tyr-122' of R2 and R1.
Miscellaneous	S.typhimurium produces two separate class I enzymes. This one is the functional enzyme during growth.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase large chain family. Contains 1 ATP-cone domain.

Ontologies

Keywords
Biological process	DNA replication
Ligand	ATP-binding Nucleotide-binding
Molecular function	Oxidoreductase
PTM	Disulfide bond
Technical term	Allosteric enzyme Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from electronic annotation. Source: UniProtKB-UniPathway
Cellular_component	ribonucleoside-diphosphate reductase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor 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 – 761	761	Ribonucleoside-diphosphate reductase 1 subunit alpha		PRO_0000187213
Regions
	Domain	5 – 95	91	ATP-cone
	Region	15 – 21	7	Allosteric activator binding By similarity
	Region	224 – 225	2	Substrate binding By similarity
	Region	437 – 441	5	Substrate binding By similarity
	Region	621 – 625	5	Substrate binding By similarity
Sites
	Active site	437	1	Proton acceptor By similarity
	Active site	439	1	Cysteine radical intermediate By similarity
	Active site	441	1	Proton acceptor By similarity
	Binding site	9	1	Allosteric activator By similarity
	Binding site	55	1	Allosteric activator By similarity
	Binding site	91	1	Allosteric activator By similarity
	Binding site	209	1	Substrate By similarity
	Binding site	253	1	Substrate; via amide nitrogen By similarity
	Site	225	1	Important for hydrogen atom transfer By similarity
	Site	232	1	Allosteric effector binding By similarity
	Site	262	1	Allosteric effector binding By similarity
	Site	462	1	Important for hydrogen atom transfer By similarity
	Site	730	1	Important for electron transfer By similarity
	Site	731	1	Important for electron transfer By similarity
	Site	754	1	Interacts with thioredoxin/glutaredoxin By similarity
	Site	759	1	Interacts with thioredoxin/glutaredoxin By similarity
Amino acid modifications
	Disulfide bond	225 ↔ 462		Redox-active By similarity

Sequences

	Sequence		Length	Mass (Da)
	P37426 [UniParc]. Last modified October 1, 1994. Version 1. Checksum: 0B3322D847CC58F9	FASTA	761	85,736
	10 20 30 40 50 60 MNQSLLVTKR DGRTERINLD KIHRVLDWAA EGLNNVSVSQ VELRSHIQFY DGIKTSDIHE 70 80 90 100 110 120 TIIKAAADLI SRDAPDYQYL AARLAIFHLR KKAFGQFEPP ALYHHVVKMV ELGKYDNHLL 130 140 150 160 170 180 EDYTEEEFKQ MDSFIVHDRD MTFSYAAVKQ LEGKYLVQNR VTGEIYESAQ FLYILVAACL 190 200 210 220 230 240 FSNYPRETRL DYVKRFYDAV STFKISLPTP IMSGVRTPTR QFSSCVLIEC GDSLDSINAT 250 260 270 280 290 300 SSAIVKYVSQ RAGIGINAGR IRALGSPIRG GEAFHTGCIP FYKHFQTAVK SCSQGGVRGG 310 320 330 340 350 360 AATLFYPMWH LEVESLLVLK NNRGVEGNRV RHMDYGVQIN KLMYTRLLKG GDITLFSPSD 370 380 390 400 410 420 VPGLYDAFFA DQDEFERLYV KYEHDDSIRK QRVKAVELFS LMMQERASTG RIYIQNVDHC 430 440 450 460 470 480 NTHSPFDPVV APVRQSNLCL EIALPTKPLN DVNDENGEIA LCTLSAFNLG AIKTLDELEE 490 500 510 520 530 540 LAILAVRALD ALLDYQDYPI PAAKRGAMGR RTLGIGVINF AYWLAKNGKR YSDGSANNLT 550 560 570 580 590 600 HKTFEAIQYY LLKASNELAK EQGACPWFNE TTYAKGILPI DTYKKDLDAI VNEPLHYDWE 610 620 630 640 650 660 QLRESIKTHG LRNSTLSALM PSETSSQISN ATNGIEPPRG YVSIKASKDG ILRQVVPDYE 670 680 690 700 710 720 HLKDAYELLW EMPNNDGYLQ LVGIMQKFID QSISANTNYD PSRFPSGKVP MQQLLKDLLT 730 740 750 760 AYKFGVKTLY YQNTRDGAED AQDDLAPSIQ DDGCESGACK I

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Cloning and sequencing of the genes from Salmonella typhimurium encoding a new bacterial ribonucleotide reductase." Jordan A., Gibert I., Barbe J. J. Bacteriol. 176:3420-3427(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: LT2.
[2]	"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2." McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K. Nature 413:852-856(2001) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: LT2 / SGSC1412 / ATCC 700720.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X72948 Genomic DNA. Translation: CAA51452.1. AE006468 Genomic DNA. Translation: AAL21178.1.
PIR	S32629.
RefSeq	NP_461219.1. NC_003197.1.
3D structure databases
ProteinModelPortal	P37426.
SMR	P37426. Positions 5-737.
ModBase	Search...
Protein-protein interaction databases
STRING	99287.STM2277.
Proteomic databases
PaxDb	P37426.
PRIDE	P37426.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	AAL21178; AAL21178; STM2277.
GeneID	1253799.
KEGG	stm:STM2277.
PATRIC	32383161. VBISalEnt20916_2410.
Phylogenomic databases
eggNOG	COG0209.
HOGENOM	HOG000278076.
KO	K00525.
OMA	YKYGVKT.
ProtClustDB	PRK09103.
Enzyme and pathway databases
UniPathway	UPA00326.
Family and domain databases
InterPro	IPR005144. ATP-cone. IPR013346. NrdE_NrdA. IPR000788. RNR_lg_C. IPR013509. RNR_lsu_N. IPR008926. RNR_R1-su_N. [Graphical view]
Pfam	PF03477. ATP-cone. 1 hit. PF02867. Ribonuc_red_lgC. 1 hit. PF00317. Ribonuc_red_lgN. 1 hit. [Graphical view]
PRINTS	PR01183. RIBORDTASEM1.
SUPFAM	SSF48168. Ribonucleo_red_N. 1 hit.
TIGRFAMs	TIGR02506. NrdE_NrdA. 1 hit.
PROSITE	PS51161. ATP_CONE. 1 hit. PS00089. RIBORED_LARGE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RIR1_SALTY

Accession

Primary (citable) accession number: P37426

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	May 1, 2013
This is version 107 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program