O31875 (NRDEB_BACSU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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

Alternative name(s):
Ribonucleotide reductase large subunit

Cleaved into the following chain:

1. Bsu nrdEB intein

Gene names

Name:	nrdEB
Synonyms:	yojP, yosN
Ordered Locus Names:	BSU20060

Organism

Bacillus subtilis (strain 168) [Reference proteome] [HAMAP]

Taxonomic identifier

224308 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Firmicutes › Bacilli › Bacillales › Bacillaceae › Bacillus › Bacillus subtilis group › Bacillus subtilis › Bacillus subtilis subsp. subtilis

Protein attributes

Sequence length	1084 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
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 By similarity.
Catalytic activity	2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.
Enzyme regulation	Under complex allosteric control mediated by deoxynucleoside triphosphates and ATP binding. 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 By similarity.
Pathway	Genetic information processing; DNA replication.
Subunit structure	Tetramer of two alpha and two beta subunits By similarity.
Post-translational modification	This protein undergoes protein self-splicing that involves post-translational excision of the intervening region (intein) followed by peptide ligation Probable.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase large chain family. Contains 1 DOD-type homing endonuclease domain.

Ontologies

Keywords
Biological process	DNA replication
Ligand	ATP-binding Nucleotide-binding
Molecular function	Oxidoreductase
PTM	Autocatalytic cleavage Disulfide bond Protein splicing
Technical term	Allosteric enzyme Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA replication Inferred from electronic annotation. Source: UniProtKB-UniPathway intein-mediated protein splicing Inferred from electronic annotation. Source: InterPro
Cellular_component	ribonucleoside-diphosphate reductase complex Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW endonuclease activity Inferred from electronic annotation. Source: InterPro 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 – 380	380	Ribonucleoside-diphosphate reductase NrdEB subunit alpha, 1st part		PRO_0000377530
	Chain	381 – 765	385	Bsu nrdEB intein		PRO_0000377531
	Chain	766 – 1084	319	Ribonucleoside-diphosphate reductase NrdEB subunit alpha, 2nd part		PRO_0000377532
Regions
	Domain	503 – 654	152	DOD-type homing endonuclease
	Region	168 – 169	2	Substrate binding By similarity
	Region	964 – 968	5	Substrate binding By similarity
Sites
	Active site	379	1	Proton acceptor Potential
	Active site	381	1	Cysteine radical intermediate Potential
	Active site	768	1	Proton acceptor Potential
	Binding site	152	1	Substrate By similarity
	Binding site	197	1	Substrate; via amide nitrogen By similarity
	Site	169	1	Important for hydrogen atom transfer By similarity
	Site	176	1	Allosteric effector binding By similarity
	Site	206	1	Allosteric effector binding By similarity
	Site	793	1	Important for hydrogen atom transfer By similarity
	Site	1067	1	Important for electron transfer By similarity
	Site	1068	1	Important for electron transfer By similarity
	Site	1079	1	Interacts with thioredoxin/glutaredoxin By similarity
	Site	1082	1	Interacts with thioredoxin/glutaredoxin By similarity
Amino acid modifications
	Disulfide bond	169 ↔ 793		Redox-active By similarity

Sequences

	Sequence		Length	Mass (Da)
	O31875 [UniParc]. Last modified October 1, 2003. Version 2. Checksum: A89CFDF93218FC61	FASTA	1,084	124,621
	10 20 30 40 50 60 MTNTIPNWIK LNNEIMIQKD GKYQFEKDKE AVHSYFVDYI NQNTVFFHDL KEKLDYLIKN 70 80 90 100 110 120 DYYEEEFLSK YTFEQIKSIY KIAYSYKFRF PSFMSAFKFY NDYALKTNDK TKILERYEDR 130 140 150 160 170 180 VSIVALYCAD GDYEKAVEEV HTMMKQEYQP ATPTFLNAGR KRRGEMVSCF LLEVGDSLND 190 200 210 220 230 240 ISRAIDISMQ LSKLGGGVAL NLNKLRAKGE AIKDVENATK GVVGVMKLLD NAFRYADQMG 250 260 270 280 290 300 QRQGSGAVYL SVFHPDITDF LDTKKISADE DVRVKTLSIG VVVPDKFIEL AREDKDYYMF 310 320 330 340 350 360 YPHSVYKEYG QYLDELDINE MYDELVENPR VRKAKGNARK LLEQLAILRS ESGYPYIMFA 370 380 390 400 410 420 DNVNKVHPNE HISKVKFSNL CVTGETLLLT ENGYEKAADL YKKQNDLKVV IDNRTKDFAV 430 440 450 460 470 480 GSKGTTIVDA IPMQLTKKDA EIFKVKTKQG YEIRATEWHK FYVKRDGEIQ KLQLNQLKTG 490 500 510 520 530 540 DKLLVQSAEG AYGKIHEPDL AYIMGIIAGD GTITEKTAKI YLYDNKKVLE QKVTDAVHRI 550 560 570 580 590 600 IQKHKVDRAY KHNTSLLPTF NMANPEKQDL LYMNSTVLFD ILKKFGMNKE TKTRVPEFIF 610 620 630 640 650 660 QANKETQAAY LSGLFQTDGC VNANHKAKAL TIELTSIHYE SLQDVQKLLL NMGVYTTIYS 670 680 690 700 710 720 NNKRSQELLP DGKGGSKLYN VKPTHKISIQ DRNSRELFMS IVEMKEYDVY KFNLLTETLQ 730 740 750 760 770 780 PKSRKPKHDF TAEIISIEED GVEDVYDTTQ EDYHSLIFNG IVTGNCSEVL QSSQVSVYTD 790 800 810 820 830 840 YDKEDEIGLD ISCNLGSMNI VNVMSNQSIA STVRIAIDSL TTVTRKTNIV NAPAVARANT 850 860 870 880 890 900 LMRSIGLGQM NLHGFLAQNN IAYESEEAKD FANTYFMMVN FYSLQRSMEI ARETGETYYK 910 920 930 940 950 960 FDGSTYKSGE YFEKYVTNDY SPQYEKVKKL FGDQHIPNIQ DWMKLKEDVM KYGLYHSYRQ 970 980 990 1000 1010 1020 AIAPTGSISY VQSSTAGVMP IMERIEERTY GNSKTYYPMP GLSAQNWFFY KEAYDMDMFK 1030 1040 1050 1060 1070 1080 VVDLIATIQQ HVDQGISFTL FLKDTMTTRD LNRIDLYAHH RGIKTLYYAR TKDTTQEGCL SCVV

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The complete genome sequence of the Gram-positive bacterium Bacillus subtilis." Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V. , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A. Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: 168.
[2]	"From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later." Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A., Vallenet D., Wang T., Moszer I., Medigue C., Danchin A. Microbiology 155:1758-1775(2009) [PubMed] [Europe PMC] [Abstract] Cited for: SEQUENCE REVISION TO C-TERMINUS.
[3]	"An 8 kb nucleotide sequence at the 3' flanking region of the sspC gene (184 degrees) on the Bacillus subtilis 168 chromosome containing an intein and an intron." Ghim S.-Y., Choi S.-K., Shin B.-S., Park S.-H. DNA Res. 5:121-126(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 424-1084. Strain: 168.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AL009126 Genomic DNA. Translation: CAB13898.2. AF012906 Genomic DNA. Translation: AAB92484.1.
PIR	H69926.
RefSeq	NP_389888.2. NC_000964.3.
3D structure databases
HSSP	HSSP built from PDB template 1PEQ based on UniProtKB Q08698.
ProteinModelPortal	O31875.
SMR	O31875. Positions 374-466, 731-766.
ModBase	Search...
Protein-protein interaction databases
STRING	224308.BSU20060.
Proteomic databases
PaxDb	O31875.
PRIDE	O31875.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	CAB13898; CAB13898; BSU20060.
GeneID	939475.
KEGG	bsu:BSU20060.
PATRIC	18975859. VBIBacSub10457_2120.
Organism-specific databases
GenoList	BSU20060. [Micado]
Phylogenomic databases
eggNOG	COG0209.
HOGENOM	HOG000113851.
KO	K00525.
OMA	ELDINEM.
ProtClustDB	CLSK739693.
Enzyme and pathway databases
BioCyc	BSUB:BSU20060-MONOMER.
UniPathway	UPA00326.
Family and domain databases
InterPro	IPR003586. Hint_dom_C. IPR003587. Hint_dom_N. IPR006142. INTEIN. IPR004042. Intein_endonuc. IPR006141. Intein_splice_site. IPR000788. RNR_lg_C. IPR013509. RNR_lsu_N. IPR013554. RNR_N. IPR008926. RNR_R1-su_N. [Graphical view]
Pfam	PF02867. Ribonuc_red_lgC. 2 hits. PF00317. Ribonuc_red_lgN. 1 hit. PF08343. RNR_N. 1 hit. [Graphical view]
PRINTS	PR00379. INTEIN.
SMART	SM00305. HintC. 1 hit. SM00306. HintN. 1 hit. [Graphical view]
SUPFAM	SSF48168. Ribonucleo_red_N. 1 hit.
TIGRFAMs	TIGR01443. intein_Cterm. 1 hit. TIGR01445. intein_Nterm. 1 hit.
PROSITE	PS50818. INTEIN_C_TER. 1 hit. PS50819. INTEIN_ENDONUCLEASE. 1 hit. PS50817. INTEIN_N_TER. 1 hit. PS00089. RIBORED_LARGE. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

NRDEB_BACSU

Accession

Primary (citable) accession number: O31875
Secondary accession number(s): Q7BVQ5

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 16, 2009
Last sequence update:	October 1, 2003
Last modified:	May 1, 2013
This is version 90 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program