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Entry version 154 (25 May 2022)
Sequence version 2 (01 Nov 1997)
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Protein

NADP-dependent 3-hydroxy acid dehydrogenase YdfG

Gene

ydfG

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

NADP-dependent dehydrogenase with broad substrate specificity acting on 3-hydroxy acids. Catalyzes the NADP-dependent oxidation of L-allo-threonine to L-2-amino-3-keto-butyrate, which is spontaneously decarboxylated into aminoacetone. Also acts on D-threonine, L-serine, D-serine, D-3-hydroxyisobutyrate, L-3-hydroxyisobutyrate, D-glycerate and L-glycerate (PubMed:12535615).

Able to catalyze the reduction of the malonic semialdehyde to 3-hydroxypropionic acid. YdfG is apparently supplementing RutE, the presumed malonic semialdehyde reductase involved in pyrimidine degradation since both are able to detoxify malonic semialdehyde (PubMed:20400551).

2 Publications

Miscellaneous

L-threonine, D-allo-threonine, DL-threo-3-phenyl-serine, malonate, DL-malate, citrate, isocitrate, DL-lactate, DL-tartrate, gluconate, glycerol and glycolate are inert as substrates.

<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>Kineticsi

The highest catalytic efficiency was observed with L-allo-threonine.1 Publication
  1. KM=0.54 mM for NADP+ (at pH 9 and at 30 degrees Celsius)1 Publication
  2. KM=40 mM for L-serine (at pH 9 and at 30 degrees Celsius)1 Publication
  3. KM=69 mM for D-serine (at pH 9 and at 30 degrees Celsius)1 Publication
  4. KM=60 mM for D-threonine (at pH 9 and at 30 degrees Celsius)1 Publication
  5. KM=29 mM for L-allo-threonine (at pH 9 and at 30 degrees Celsius)1 Publication
  6. KM=33 mM for L-glycerate (at pH 9 and at 30 degrees Celsius)1 Publication
  7. KM=50 mM for D-glycerate (at pH 9 and at 30 degrees Celsius)1 Publication
  8. KM=60 mM for L-3-hydroxyisobutyrate (at pH 9 and at 30 degrees Celsius)1 Publication
  9. KM=61 mM for D-3-hydroxyisobutyrate (at pH 9 and at 30 degrees Celsius)1 Publication

pH dependencei

Optimum pH is about 8.5 for the oxidation of L-serine. Stable from pH 6.5 to 10.0.1 Publication

Temperature dependencei

Still active after heating at 55 degrees Celsius for 80 minutes.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>Binding sitei81NADP; via carbonyl oxygenBy similarity1
Binding sitei134SubstrateBy similarity1
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section is used for enzymes and indicates the residues directly involved in catalysis.<p><a href='/help/act_site' target='_top'>More...</a></p>Active sitei147Proton acceptorPROSITE-ProRule annotation1
Binding sitei147NADPBy similarity1
Binding sitei151NADPBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi7 – 12NADPBy similarity6
Nucleotide bindingi32 – 33NADPBy similarity2
Nucleotide bindingi54 – 55NADPBy similarity2
Nucleotide bindingi177 – 185NADPBy similarity9

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionOxidoreductase
LigandNADP

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:EG12345-MONOMER

BRENDA Comprehensive Enzyme Information System

More...
BRENDAi
1.1.1.381, 2026

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
NADP-dependent 3-hydroxy acid dehydrogenase YdfG1 Publication
Alternative name(s):
L-allo-threonine dehydrogenase1 Publication (EC:1.1.1.3811 Publication)
Malonic semialdehyde reductase1 Publication (EC:1.1.1.2981 Publication)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:ydfGImported
Ordered Locus Names:b1539, JW1532
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

Cells lacking this gene grow poorly on pyrimidine nucleosides and bases as the sole source of nitrogen at room temperature indicating a probably accumulation of a toxic intermediate, the malonic semialdehyde.1 Publication

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000548251 – 248NADP-dependent 3-hydroxy acid dehydrogenase YdfGAdd BLAST248

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P39831

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P39831

PRoteomics IDEntifications database

More...
PRIDEi
P39831

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homotetramer.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
4261740, 23 interactors
850445, 1 interactor

Database of interacting proteins

More...
DIPi
DIP-11696N

Protein interaction database and analysis system

More...
IntActi
P39831, 13 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b1539

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

AlphaFold Protein Structure Database

More...
AlphaFoldDBi
P39831

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P39831

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
COG4221, Bacteria

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_010194_2_10_6

InParanoid: Eukaryotic Ortholog Groups

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InParanoidi
P39831

Identification of Orthologs from Complete Genome Data

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OMAi
WRWMWET

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P39831

Family and domain databases

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR036291, NAD(P)-bd_dom_sf
IPR020904, Sc_DH/Rdtase_CS
IPR002347, SDR_fam

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00106, adh_short, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00081, GDHRDH
PR00080, SDRFAMILY

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51735, SSF51735, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00061, ADH_SHORT, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

P39831-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MIVLVTGATA GFGECITRRF IQQGHKVIAT GRRQERLQEL KDELGDNLYI
60 70 80 90 100
AQLDVRNRAA IEEMLASLPA EWCNIDILVN NAGLALGMEP AHKASVEDWE
110 120 130 140 150
TMIDTNNKGL VYMTRAVLPG MVERNHGHII NIGSTAGSWP YAGGNVYGAT
160 170 180 190 200
KAFVRQFSLN LRTDLHGTAV RVTDIEPGLV GGTEFSNVRF KGDDGKAEKT
210 220 230 240
YQNTVALTPE DVSEAVWWVS TLPAHVNINT LEMMPVTQSY AGLNVHRQ
Length:248
Mass (Da):27,249
Last modified:November 1, 1997 - v2
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i6FECC5FBAA86EA42
GO

<p>This subsection of the 'Sequence' section reports difference(s) between the protein sequence shown in the UniProtKB entry and other available protein sequences derived from the same gene.<p><a href='/help/sequence_caution' target='_top'>More...</a></p>Sequence cautioni

The sequence X57947 differs from that shown. Reason: Frameshift.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti182G → T in X57947 (PubMed:8226676).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74612.1
AP009048 Genomic DNA Translation: BAA15241.1
X57947 Genomic DNA No translation available.

Protein sequence database of the Protein Information Resource

More...
PIRi
F64908

NCBI Reference Sequences

More...
RefSeqi
NP_416057.1, NC_000913.3
WP_000636571.1, NZ_STEB01000003.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC74612; AAC74612; b1539
BAA15241; BAA15241; BAA15241

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
66674600
946085

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW1532
eco:b1539

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.726

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74612.1
AP009048 Genomic DNA Translation: BAA15241.1
X57947 Genomic DNA No translation available.
PIRiF64908
RefSeqiNP_416057.1, NC_000913.3
WP_000636571.1, NZ_STEB01000003.1

3D structure databases

AlphaFoldDBiP39831
SMRiP39831
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi4261740, 23 interactors
850445, 1 interactor
DIPiDIP-11696N
IntActiP39831, 13 interactors
STRINGi511145.b1539

Proteomic databases

jPOSTiP39831
PaxDbiP39831
PRIDEiP39831

Genome annotation databases

EnsemblBacteriaiAAC74612; AAC74612; b1539
BAA15241; BAA15241; BAA15241
GeneIDi66674600
946085
KEGGiecj:JW1532
eco:b1539
PATRICifig|1411691.4.peg.726

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB2249

Phylogenomic databases

eggNOGiCOG4221, Bacteria
HOGENOMiCLU_010194_2_10_6
InParanoidiP39831
OMAiWRWMWET
PhylomeDBiP39831

Enzyme and pathway databases

BioCyciEcoCyc:EG12345-MONOMER
BRENDAi1.1.1.381, 2026

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P39831

Family and domain databases

InterProiView protein in InterPro
IPR036291, NAD(P)-bd_dom_sf
IPR020904, Sc_DH/Rdtase_CS
IPR002347, SDR_fam
PfamiView protein in Pfam
PF00106, adh_short, 1 hit
PRINTSiPR00081, GDHRDH
PR00080, SDRFAMILY
SUPFAMiSSF51735, SSF51735, 1 hit
PROSITEiView protein in PROSITE
PS00061, ADH_SHORT, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiYDFG_ECOLI
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P39831
Secondary accession number(s): P77149, P78161, P78162
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: November 1, 1997
Last modified: May 25, 2022
This is version 154 of the entry and version 2 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
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