Reviewed, UniProtKB/Swiss-Prot P00452 (RIR1_ECOLI)

Names and origin

Protein names

Recommended name:
    Ribonucleoside-diphosphate reductase 1 subunit alpha
    EC=1.17.4.1
Alternative name(s):
    Ribonucleoside-diphosphate reductase 1 R1 subunit
    Ribonucleotide reductase 1
    Protein B1

Gene names

Name:	nrdA
Synonyms:	dnaF
Ordered Locus Names:	b2234, JW2228

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	761 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

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. It also provides redox-active cysteines.
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. In vitro, its activity is increased by dithiothreitol (DTT) or thioredoxins (non-specific).
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.
Post-translational modification	Binding of the substrate occurs primarily when the active-site cysteines are reduced.
Miscellaneous	E.coli produces two separate class I enzymes. This one is the functional enzyme during growth. Two distinct regulatory sites have been defined: one controls substrate specificity and the other regulates the overall catalytic activity. A substrate-binding catalytic site, located on R1, is formed only in the presence of the second subunit R2.
Sequence similarities	Belongs to the ribonucleoside diphosphate reductase large chain family. Contains 1 ATP-cone domain.
Sequence caution	The sequence AAA24223.1 differs from that shown. Reason: Miscellaneous discrepancy.

Ontologies

Keywords
Biological process	DNA replication
Coding sequence diversity	Alternative initiation
Ligand	ATP-binding Nucleotide-binding
Molecular function	Oxidoreductase
PTM	Acetylation Disulfide bond
Technical term	3D-structure Allosteric enzyme Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW deoxyribonucleotide biosynthetic process Inferred from direct assay. Source: UniProtKB nucleobase, nucleoside and nucleotide interconversion Inferred from direct assay. Source: UniProtKB oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	ribonucleoside-diphosphate reductase complex Inferred from direct assay. Source: UniProtKB
Molecular function	ATP binding Inferred from direct assay. Source: UniProtKB protein binding Inferred from physical interaction. Source: IntAct ribonucleoside-diphosphate reductase activity Inferred from direct assay. Source: UniProtKB
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
bglX	P33363	1	EBI-370018,EBI-1114600

Alternative products

This entry describes 2 isoforms produced by alternative initiation. [Align] [Select]

Isoform Alpha (identifier: P00452-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform Alpha' (identifier: P00452-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-25: Missing.
     26-26: L → M

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_0000030596

Regions

Domain

5 – 95

91

ATP-cone

Region

15 – 21

7

Allosteric activator binding

Region

224 – 225

2

Substrate binding By similarity

Region

437 – 441

5

Substrate binding By similarity

Region

621 – 625

5

Substrate binding

Sites

Active site

437

1

Proton acceptor Ref.8 Ref.9 Ref.12

Active site

439

1

Cysteine radical intermediate

Active site

441

1

Proton acceptor Ref.8 Ref.9 Ref.12

Binding site

9

1

Allosteric activator

Binding site

55

1

Allosteric activator

Binding site

91

1

Allosteric activator

Binding site

209

1

Substrate

Binding site

253

1

Substrate; via amide nitrogen By similarity

Site

225

1

Important for hydrogen atom transfer

Site

232

1

Allosteric effector binding

Site

262

1

Allosteric effector binding

Site

462

1

Important for hydrogen atom transfer

Site

730

1

Important for electron transfer

Site

731

1

Important for electron transfer

Site

754

1

Interacts with thioredoxin/glutaredoxin

Site

759

1

Interacts with thioredoxin/glutaredoxin

Amino acid modifications

Modified residue

283

1

N6-acetyllysine Ref.10

Disulfide bond

225 ↔ 462

Redox-active

Natural variations

Alternative sequence

1 – 25

25

Missing in isoform Alpha'.

VSP_018871

Alternative sequence

26

1

L → M in isoform Alpha'.

VSP_018872

Natural variant

1 – 2

2

Missing in 15% of the chains.

Natural variant

1

1

Missing in 30% of the chains.

Experimental info

Mutagenesis

441

1

E → A or Q: Loss of activity. Ref.12

Mutagenesis

441

1

E → D: Decrease in activity. Ref.12

Mutagenesis

730

1

Y → F: Loss of activity. Ref.9

Mutagenesis

731

1

Y → F: Loss of activity. Ref.9

Secondary structure

1

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761

Helix Strand Turn

Details...

Beta strand

6 – 8

3

Beta strand

14 – 16

3

Helix

19 – 30

12

Helix

38 – 46

9

Helix

55 – 68

14

Helix

77 – 94

18

Beta strand

95 – 98

4

Helix

102 – 111

10

Helix

118 – 122

5

Helix

125 – 132

8

Helix

137 – 142

6

Helix

145 – 154

10

Turn

160 – 163

4

Helix

169 – 180

12

Turn

181 – 183

3

Turn

186 – 188

3

Helix

189 – 201

13

Beta strand

204 – 206

3

Helix

209 – 214

6

Beta strand

225 – 229

5

Helix

234 – 248

15

Turn

249 – 251

3

Beta strand

253 – 257

5

Helix

278 – 289

12

Turn

290 – 292

3

Beta strand

296 – 299

4

Beta strand

302 – 307

6

Helix

313 – 316

4

Turn

317 – 320

4

Beta strand

322 – 324

3

Helix

326 – 328

3

Beta strand

333 – 339

7

Helix

341 – 349

9

Beta strand

352 – 356

5

Helix

358 – 360

3

Helix

364 – 370

7

Helix

372 – 384

13

Beta strand

390 – 394

5

Helix

395 – 409

15

Beta strand

412 – 416

5

Helix

417 – 422

6

Beta strand

423 – 426

4

Turn

428 – 430

3

Beta strand

463 – 468

6

Helix

475 – 477

3

Helix

478 – 495

18

Helix

501 – 510

10

Beta strand

513 – 518

6

Helix

520 – 526

7

Helix

537 – 562

26

Helix

568 – 570

3

Helix

573 – 575

3

Helix

579 – 582

4

Helix

585 – 589

5

Helix

599 – 609

11

Helix

624 – 628

5

Beta strand

639 – 646

8

Beta strand

648 – 655

8

Helix

659 – 662

4

Turn

663 – 665

3

Helix

669 – 671

3

Helix

676 – 688

13

Beta strand

697 – 699

3

Helix

701 – 703

3

Helix

705 – 707

3

Helix

711 – 723

13

Beta strand

732 – 734

3

Helix

738 – 741

4

Sequences

	Sequence		Length	Mass (Da)
	Isoform Alpha [UniParc]. Last modified November 1, 1997. Version 2. Checksum: 7E034F154567C3FC	FASTA	761	85,775
	10 20 30 40 50 60 MNQNLLVTKR DGSTERINLD KIHRVLDWAA EGLHNVSISQ VELRSHIQFY DGIKTSDIHE 70 80 90 100 110 120 TIIKAAADLI SRDAPDYQYL AARLAIFHLR KKAYGQFEPP ALYDHVVKMV EMGKYDNHLL 130 140 150 160 170 180 EDYTEEEFKQ MDTFIDHDRD MTFSYAAVKQ LEGKYLVQNR VTGEIYESAQ FLYILVAACL 190 200 210 220 230 240 FSNYPRETRL QYVKRFYDAV 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 EDITLFSPSD 370 380 390 400 410 420 VPGLYDAFFA DQEEFERLYT KYEKDDSIRK QRVKAVELFS LMMQERASTG RIYIQNVDHC 430 440 450 460 470 480 NTHSPFDPAI APVRQSNLCL EIALPTKPLN DVNDENGEIA LCTLSAFNLG AINNLDELEE 490 500 510 520 530 540 LAILAVRALD ALLDYQDYPI PAAKRGAMGR RTLGIGVINF AYYLAKHGKR YSDGSANNLT 550 560 570 580 590 600 HKTFEAIQYY LLKASNELAK EQGACPWFNE TTYAKGILPI DTYKKDLDTI ANEPLHYDWE 610 620 630 640 650 660 ALRESIKTHG LRNSTLSALM PSETSSQISN ATNGIEPPRG YVSIKASKDG ILRQVVPDYE 670 680 690 700 710 720 HLHDAYELLW EMPGNDGYLQ LVGIMQKFID QSISANTNYD PSRFPSGKVP MQQLLKDLLT 730 740 750 760 AYKFGVKTLY YQNTRDGAED AQDDLVPSIQ DDGCESGACK I
	Isoform Alpha'. Checksum: 498ADEDC2154C084	FASTA	736	82,860
	10 20 30 40 50 60 MDWAAEGLHN VSISQVELRS HIQFYDGIKT SDIHETIIKA AADLISRDAP DYQYLAARLA 70 80 90 100 110 120 IFHLRKKAYG QFEPPALYDH VVKMVEMGKY DNHLLEDYTE EEFKQMDTFI DHDRDMTFSY 130 140 150 160 170 180 AAVKQLEGKY LVQNRVTGEI YESAQFLYIL VAACLFSNYP RETRLQYVKR FYDAVSTFKI 190 200 210 220 230 240 SLPTPIMSGV RTPTRQFSSC VLIECGDSLD SINATSSAIV KYVSQRAGIG INAGRIRALG 250 260 270 280 290 300 SPIRGGEAFH TGCIPFYKHF QTAVKSCSQG GVRGGAATLF YPMWHLEVES LLVLKNNRGV 310 320 330 340 350 360 EGNRVRHMDY GVQINKLMYT RLLKGEDITL FSPSDVPGLY DAFFADQEEF ERLYTKYEKD 370 380 390 400 410 420 DSIRKQRVKA VELFSLMMQE RASTGRIYIQ NVDHCNTHSP FDPAIAPVRQ SNLCLEIALP 430 440 450 460 470 480 TKPLNDVNDE NGEIALCTLS AFNLGAINNL DELEELAILA VRALDALLDY QDYPIPAAKR 490 500 510 520 530 540 GAMGRRTLGI GVINFAYYLA KHGKRYSDGS ANNLTHKTFE AIQYYLLKAS NELAKEQGAC 550 560 570 580 590 600 PWFNETTYAK GILPIDTYKK DLDTIANEPL HYDWEALRES IKTHGLRNST LSALMPSETS 610 620 630 640 650 660 SQISNATNGI EPPRGYVSIK ASKDGILRQV VPDYEHLHDA YELLWEMPGN DGYLQLVGIM 670 680 690 700 710 720 QKFIDQSISA NTNYDPSRFP SGKVPMQQLL KDLLTAYKFG VKTLYYQNTR DGAEDAQDDL 730 VPSIQDDGCE SGACKI

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Primary structure of the Escherichia coli ribonucleoside diphosphate reductase operon." Carlson J., Fuchs J.A., Messing J. Proc. Natl. Acad. Sci. U.S.A. 81:4294-4297(1984) [PubMed: 6087316] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]	"Nucleotide sequence of the gene coding for the large subunit of ribonucleotide reductase of Escherichia coli. Correction." Nilsson O., Aaberg A., Lundqvist T., Sjoeberg B.-M. Nucleic Acids Res. 16:4174-4174(1988) [PubMed: 3287341] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[3]	Sjoeberg B.-M. Submitted (APR-2004) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION TO 526-527.
[4]	"Construction of a contiguous 874-kb sequence of the Escherichia coli-K12 genome corresponding to 50.0-68.8 min on the linkage map and analysis of its sequence features." Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T., Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K., Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T. , Oyama S., Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H., Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T. DNA Res. 4:91-113(1997) [PubMed: 9205837] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[6]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[7]	"Protein B1 of ribonucleotide reductase. Direct analytical data and comparisons with data indirectly deduced from the nucleotide sequence of the Escherichia coli nrdA gene." Sjoeberg B.-M., Eriksson S., Joernvall H., Carlquist M., Eklund H. Eur. J. Biochem. 150:423-427(1985) [PubMed: 3894026] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE.
[8]	"Evidence for two different classes of redox-active cysteines in ribonucleotide reductase of Escherichia coli." Aaberg A., Hahne S., Karlsson M., Larsson A., Ormoe M., Aahgren A., Sjoeberg B.-M. J. Biol. Chem. 264:12249-12252(1989) [PubMed: 2663852] [Abstract] Cited for: ACTIVE SITES.
[9]	"Two conserved tyrosine residues in protein R1 participate in an intermolecular electron transfer in ribonucleotide reductase." Ekberg M., Sahlin M., Eriksson M., Sjoberg B.M. J. Biol. Chem. 271:20655-20659(1996) [PubMed: 8702814] [Abstract] Cited for: ACTIVE SITES, MUTAGENESIS OF TYR-730 AND TYR-731.
[10]	"Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y. Mol. Cell. Proteomics 8:215-225(2009) [PubMed: 18723842] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-283, MASS SPECTROMETRY.
[11]	"Structure of ribonucleotide reductase protein R1." Uhlin U., Eklund H. Nature 370:533-539(1994) [PubMed: 8052308] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[12]	"A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase." Persson A.L., Eriksson M., Katterle B., Potsch S., Sahlin M., Sjoberg B.M. J. Biol. Chem. 272:31533-31541(1997) [PubMed: 9395490] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF MUTANTS ALA-441; ASP-441 AND GLN-441, DISULFIDE BOND, SUBUNIT, ACTIVE SITE, ENZYME REGULATION, ENZYME MECHANISM, MUTAGENESIS OF GLU-441.
[13]	"Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding." Eriksson M., Uhlin U., Ramaswamy S., Ekberg M., Regnstroem K., Sjoeberg B.-M., Eklund H. Structure 5:1077-1092(1997) [PubMed: 9309223] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS) IN COMPLEXES WITH ATP; GDP AND TTP, DISULFIDE BOND, SUBUNIT, ENZYME REGULATION.
[14]	"Binding specificity and mechanistic insight into glutaredoxin-catalyzed protein disulfide reduction." Berardi M.J., Bushweller J.H. J. Mol. Biol. 292:151-161(1999) [PubMed: 10493864] [Abstract] Cited for: STRUCTURE BY NMR OF 737-761, BINDING SITES.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

K02672 Genomic DNA. Translation: AAA24223.1. Sequence problems.
X06999 Genomic DNA. Translation: CAA30056.2.
U00096 Genomic DNA. Translation: AAC75294.1.
AP009048 Genomic DNA. Translation: BAA16053.1.

PIR

RDEC1R. H64993.

RefSeq

AP_002831.1.
NP_416737.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1QFN	NMR	-	B	737-761	[»]
1R1R	X-ray	2.90	A/B/C	1-761	[»]
1RLR	X-ray	2.50	A	1-761	[»]
2R1R	X-ray	3.00	A/B/C	1-761	[»]
3R1R	X-ray	3.00	A/B/C	1-761	[»]
4R1R	X-ray	3.20	A/B/C	1-761	[»]
5R1R	X-ray	3.10	A/B/C	1-761	[»]
6R1R	X-ray	3.10	A/B/C	1-761	[»]
7R1R	X-ray	3.10	A/B/C	1-761	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-584N.

IntAct

P00452. 9 interactions.

STRING

P00452.

Genome annotation databases

GeneID

946612.

GenomeReviews

Gene locus JW2228 in contig AP009048_GR.
Gene locus b2234 in contig U00096_GR.

KEGG

ecj:JW2228.
eco:b2234.

Organism-specific databases

EchoBASE

EB0654.

EcoGene

EG10660. nrdA.

CMR

Search...

Phylogenomic databases

eggNOG

COG0209.

HOGENOM

HBG297012.

OMA

ATLFYPL.

Enzyme and pathway databases

BioCyc

EcoCyc:NRDA-MONOMER.
ECOL168927:B2234-MONOMER.
MetaCyc:NRDA-MONOMER.

Gene expression databases

Genevestigator

P00452.

Family and domain databases

InterPro

IPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR013509. Ribncl_Rdtase_lsu_N.
IPR000788. Ribncl_red_lg_C.
IPR008926. Ribnucl_Rdtase_R1-su_N.
[Graphical view]

PANTHER

PTHR11573. Ribncl_red_lg_C. 1 hit.

Pfam

PF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]

PRINTS

PR01183. RIBORDTASEM1.

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_ECOLI

Accession

Primary (citable) accession number: P00452
Secondary accession number(s): P78088, P78177

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	November 1, 1997
Last modified:	February 9, 2010
This is version 121 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

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