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Protein

GDP-mannose pyrophosphatase NudK

Gene

nudK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of GDP-mannose. Can also use other substrates, catalyzing the hydrolysis of the pyrophosphate bond, releasing a nucleoside monophosphate and a phosphorylated moiety, depending on the substrate.1 Publication

Catalytic activityi

GDP-mannose + H2O = GMP + mannose-1-phosphate.1 Publication

Cofactori

Mg2+1 Publication

Kineticsi

  1. KM=0.81 mM for GDP-mannose1 Publication
  1. Vmax=207 µmol/min/mg enzyme with GDP-mannose as substrate1 Publication

pH dependencei

Optimum pH is about 8.5.1 Publication

GO - Molecular functioni

  • GDP-mannose hydrolase activity Source: EcoCyc
  • magnesium ion binding Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Magnesium

Enzyme and pathway databases

BioCyciEcoCyc:EG12410-MONOMER.
ECOL316407:JW2451-MONOMER.
MetaCyc:EG12410-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
GDP-mannose pyrophosphatase NudK (EC:3.6.1.-)
Gene namesi
Name:nudK
Synonyms:yffH
Ordered Locus Names:b2467, JW2451
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12410. nudK.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 191191GDP-mannose pyrophosphatase NudKPRO_0000169231Add
BLAST

Proteomic databases

PaxDbiP37128.
PRIDEiP37128.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

BioGridi4260924. 45 interactions.
IntActiP37128. 10 interactions.
STRINGi511145.b2467.

Structurei

Secondary structure

1
191
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 1410Combined sources
Beta strandi16 – 2813Combined sources
Beta strandi30 – 323Combined sources
Beta strandi34 – 4310Combined sources
Beta strandi47 – 548Combined sources
Turni55 – 584Combined sources
Beta strandi59 – 668Combined sources
Helixi68 – 714Combined sources
Turni72 – 743Combined sources
Beta strandi79 – 824Combined sources
Beta strandi84 – 874Combined sources
Helixi93 – 10412Combined sources
Beta strandi112 – 1209Combined sources
Turni122 – 1243Combined sources
Beta strandi128 – 1358Combined sources
Helixi138 – 1403Combined sources
Beta strandi152 – 1598Combined sources
Helixi160 – 16910Combined sources
Helixi175 – 18713Combined sources
Turni188 – 1903Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VIUX-ray2.40A/B/C/D2-191[»]
3O52X-ray2.50A/B/C/D/E1-191[»]
3O61X-ray2.45A/B/C/D1-191[»]
3O69X-ray2.10A/B1-191[»]
3O6ZX-ray2.05A/B1-191[»]
ProteinModelPortaliP37128.
SMRiP37128. Positions 3-191.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP37128.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini43 – 180138Nudix hydrolasePROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi86 – 10621Nudix boxAdd
BLAST

Sequence similaritiesi

Belongs to the Nudix hydrolase family. NudK subfamily.Curated
Contains 1 nudix hydrolase domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4107VIJ. Bacteria.
ENOG410YMTX. LUCA.
HOGENOMiHOG000045855.
InParanoidiP37128.
KOiK12945.
OMAiCIRRETE.
PhylomeDBiP37128.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR004385. NDP_pyrophosphatase.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR00052. TIGR00052. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P37128-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTQQITLIKD KILSDNYFTL HNITYDLTRK DGEVIRHKRE VYDRGNGATI
60 70 80 90 100
LLYNTKKKTV VLIRQFRVAT WVNGNESGQL IESCAGLLDN DEPEVCIRKE
110 120 130 140 150
AIEETGYEVG EVRKLFELYM SPGGVTELIH FFIAEYSDNQ RANAGGGVED
160 170 180 190
EDIEVLELPF SQALEMIKTG EIRDGKTVLL LNYLQTSHLM D
Length:191
Mass (Da):21,749
Last modified:November 1, 1997 - v2
Checksum:i13880625B41233C5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75520.1.
AP009048 Genomic DNA. Translation: BAA16341.1.
L34011 Genomic DNA. Translation: AAB46945.1.
PIRiB65022.
RefSeqiNP_416962.1. NC_000913.3.
WP_001300814.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75520; AAC75520; b2467.
BAA16341; BAA16341; BAA16341.
GeneIDi947072.
KEGGiecj:JW2451.
eco:b2467.
PATRICi32120317. VBIEscCol129921_2561.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC75520.1.
AP009048 Genomic DNA. Translation: BAA16341.1.
L34011 Genomic DNA. Translation: AAB46945.1.
PIRiB65022.
RefSeqiNP_416962.1. NC_000913.3.
WP_001300814.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1VIUX-ray2.40A/B/C/D2-191[»]
3O52X-ray2.50A/B/C/D/E1-191[»]
3O61X-ray2.45A/B/C/D1-191[»]
3O69X-ray2.10A/B1-191[»]
3O6ZX-ray2.05A/B1-191[»]
ProteinModelPortaliP37128.
SMRiP37128. Positions 3-191.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260924. 45 interactions.
IntActiP37128. 10 interactions.
STRINGi511145.b2467.

Proteomic databases

PaxDbiP37128.
PRIDEiP37128.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75520; AAC75520; b2467.
BAA16341; BAA16341; BAA16341.
GeneIDi947072.
KEGGiecj:JW2451.
eco:b2467.
PATRICi32120317. VBIEscCol129921_2561.

Organism-specific databases

EchoBASEiEB2309.
EcoGeneiEG12410. nudK.

Phylogenomic databases

eggNOGiENOG4107VIJ. Bacteria.
ENOG410YMTX. LUCA.
HOGENOMiHOG000045855.
InParanoidiP37128.
KOiK12945.
OMAiCIRRETE.
PhylomeDBiP37128.

Enzyme and pathway databases

BioCyciEcoCyc:EG12410-MONOMER.
ECOL316407:JW2451-MONOMER.
MetaCyc:EG12410-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP37128.
PROiP37128.

Family and domain databases

Gene3Di3.90.79.10. 1 hit.
InterProiIPR004385. NDP_pyrophosphatase.
IPR000086. NUDIX_hydrolase_dom.
IPR015797. NUDIX_hydrolase_dom-like.
[Graphical view]
PfamiPF00293. NUDIX. 1 hit.
[Graphical view]
SUPFAMiSSF55811. SSF55811. 1 hit.
TIGRFAMsiTIGR00052. TIGR00052. 1 hit.
PROSITEiPS51462. NUDIX. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiNUDK_ECOLI
AccessioniPrimary (citable) accession number: P37128
Secondary accession number(s): P77255
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: November 1, 1997
Last modified: September 7, 2016
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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 one 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.