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Protein

Ribonucleoside-diphosphate reductase subunit alpha

Gene

nrdA

Organism
Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity).By similarity

Catalytic activityi

2'-deoxyribonucleoside diphosphate + thioredoxin disulfide + H2O = ribonucleoside diphosphate + thioredoxin.

Enzyme regulationi

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).By similarity

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei9 – 91Allosteric activatorBy similarity
Binding sitei55 – 551Allosteric activatorBy similarity
Binding sitei91 – 911Allosteric activatorBy similarity
Binding sitei209 – 2091SubstrateBy similarity
Sitei225 – 2251Important for hydrogen atom transferBy similarity
Sitei232 – 2321Allosteric effector bindingBy similarity
Binding sitei253 – 2531Substrate; via amide nitrogenBy similarity
Sitei262 – 2621Allosteric effector bindingBy similarity
Active sitei437 – 4371Proton acceptorBy similarity
Active sitei439 – 4391Cysteine radical intermediateBy similarity
Active sitei441 – 4411Proton acceptorBy similarity
Sitei462 – 4621Important for hydrogen atom transferBy similarity
Sitei730 – 7301Important for electron transferBy similarity
Sitei731 – 7311Important for electron transferBy similarity
Sitei749 – 7491Interacts with thioredoxin/glutaredoxinBy similarity
Sitei754 – 7541Interacts with thioredoxin/glutaredoxinBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor Source: UniProtKB-EC

GO - Biological processi

  1. DNA replication Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, Nucleotide-binding

Enzyme and pathway databases

UniPathwayiUPA00326.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribonucleoside-diphosphate reductase subunit alpha (EC:1.17.4.1)
Alternative name(s):
Ribonucleotide reductase
Gene namesi
Name:nrdA
Ordered Locus Names:HI_1659
OrganismiHaemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
Taxonomic identifieri71421 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPasteurellalesPasteurellaceaeHaemophilus
ProteomesiUP000000579: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 756756Ribonucleoside-diphosphate reductase subunit alphaPRO_0000187214Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Disulfide bondi225 ↔ 462Redox-activeBy similarity

Keywords - PTMi

Disulfide bond

Proteomic databases

PRIDEiP43754.

Interactioni

Subunit structurei

Tetramer of two alpha and two beta subunits.By similarity

Protein-protein interaction databases

STRINGi71421.HI1659.

Structurei

3D structure databases

ProteinModelPortaliP43754.
SMRiP43754. Positions 5-737.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini5 – 9591ATP-conePROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni15 – 217Allosteric activator bindingBy similarity
Regioni224 – 2252Substrate bindingBy similarity
Regioni437 – 4415Substrate bindingBy similarity
Regioni621 – 6255Substrate bindingBy similarity

Sequence similaritiesi

Contains 1 ATP-cone domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiCOG0209.
KOiK00525.
OMAiYELLWQM.
OrthoDBiEOG6J48HC.
PhylomeDBiP43754.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P43754-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MNKSLMVTKR DGTQEQINLD KIHRVITWAA EGLDNVSVSQ VELRSHIQFY
60 70 80 90 100
EGIRTSDIHE TIIKAAADLI SKDSPDYQYL AARLAIFHLR KKAYGHFDPP
110 120 130 140 150
RLYDHVKKLV RMEKYDQALL DDYTREEWDT MDGFIDHWRD MTFSYAAVKQ
160 170 180 190 200
LEGKYLVQNR VTGEIYESAQ FLYLLVSASL FSKYPKETRL DYVKRFYDAT
210 220 230 240 250
STFKISLPTP IMAGVRTPTR QFSSCVLIEC DDSLDSINAT ASAIVKYVSQ
260 270 280 290 300
RAGIGINAGA IRALGSEIRG GEAFHTGCIP FYKYFQTAVK SCSQGGVRGG
310 320 330 340 350
AATLYYPIWH LEAENLLVLK NNRGVEDNRV RHMDYGVQLN KLMYQRLIKG
360 370 380 390 400
SEITLFSPSD VPGLYEAFFA DQDKFEELYV KYEQDPTIRK RTVKAVEIFS
410 420 430 440 450
LLMQERASTG RIYIQNVDHC NTHSPFDPQV APVRQSNLCL EIALPTKPLQ
460 470 480 490 500
HINDENGEIA LCTLSAFNLG KIENLDELEE LADLAVRSLD ALLDYQDYPV
510 520 530 540 550
VAAKRSSLAR RSLGIGVINY AYYLAKNGVR YSDGSANDLT HRTFEAIQYY
560 570 580 590 600
LLKASMNLAK EQGACEYFNE TTYAKGILPI DTYKKDLDSL TQEPLHYDWE
610 620 630 640 650
SLRKDIQEFG LRNSTLTALM PSETSSQISN ATNGIEPPRG HVSIKASKDG
660 670 680 690 700
ILKQVVPEYE NLMDNYELLW DIPSNDGYLH LVGIMQKFVD QAISANTNYD
710 720 730 740 750
PKRFEDGKVP MKVLLKDLLT AYKYGLKTLY YQNTRDGAED VQEDLDDGCA

GGACKI
Length:756
Mass (Da):85,696
Last modified:November 1, 1995 - v1
Checksum:i839D02FA61E185D3
GO

Sequence cautioni

The sequence AAC23305.1 differs from that shown. Reason: Erroneous initiation. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC23305.1. Different initiation.
PIRiB64135.
RefSeqiNP_439801.2. NC_000907.1.

Genome annotation databases

EnsemblBacteriaiAAC23305; AAC23305; HI_1659.
GeneIDi950495.
KEGGihin:HI1659.
PATRICi20192067. VBIHaeInf48452_1737.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L42023 Genomic DNA. Translation: AAC23305.1. Different initiation.
PIRiB64135.
RefSeqiNP_439801.2. NC_000907.1.

3D structure databases

ProteinModelPortaliP43754.
SMRiP43754. Positions 5-737.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi71421.HI1659.

Proteomic databases

PRIDEiP43754.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC23305; AAC23305; HI_1659.
GeneIDi950495.
KEGGihin:HI1659.
PATRICi20192067. VBIHaeInf48452_1737.

Phylogenomic databases

eggNOGiCOG0209.
KOiK00525.
OMAiYELLWQM.
OrthoDBiEOG6J48HC.
PhylomeDBiP43754.

Enzyme and pathway databases

UniPathwayiUPA00326.

Family and domain databases

InterProiIPR005144. ATP-cone.
IPR013346. NrdE_NrdA.
IPR000788. RNR_lg_C.
IPR013509. RNR_lsu_N.
IPR008926. RNR_R1-su_N.
[Graphical view]
PfamiPF03477. ATP-cone. 1 hit.
PF02867. Ribonuc_red_lgC. 1 hit.
PF00317. Ribonuc_red_lgN. 1 hit.
[Graphical view]
PRINTSiPR01183. RIBORDTASEM1.
SUPFAMiSSF48168. SSF48168. 1 hit.
TIGRFAMsiTIGR02506. NrdE_NrdA. 1 hit.
PROSITEiPS51161. ATP_CONE. 1 hit.
PS00089. RIBORED_LARGE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 51907 / DSM 11121 / KW20 / Rd.

Entry informationi

Entry nameiRIR1_HAEIN
AccessioniPrimary (citable) accession number: P43754
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1995
Last sequence update: November 1, 1995
Last modified: January 7, 2015
This is version 110 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Allosteric enzyme, Complete proteome, Reference proteome

Documents

  1. Haemophilus influenzae
    Haemophilus influenzae (strain Rd): entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.