Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Ureidoglycolate dehydrogenase (NAD(+))

Gene

allD

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

Functioni

AllD plays a pivotal role as a metabolic branch-point enzyme in nitrogen utilization via the assimilation of allantoin (PubMed:10601204). It is able to utilize allantoin as a sole source of nitrogen under anaerobic conditions (PubMed:10601204). Catalyzes the oxidation of ureidoglycolate to oxalurate (PubMed:23284870).2 Publications

Catalytic activityi

(S)-ureidoglycolate + NAD+ = N-carbamoyl-2-oxoglycine + NADH.1 Publication

Kineticsi

Kact is 62.39 sec(-1) for dehydrogenase activity with NAD. Kact is 57.06 sec(-1) for dehydrogenase activity with (S)-ureidoglycolate.1 Publication
  1. KM=0.56 mM for NAD1 Publication
  2. KM=1.06 mM for (S)-ureidoglycolate1 Publication

    Pathwayi: (S)-allantoin degradation

    This protein is involved in step 1 of the subpathway that synthesizes oxalurate from (S)-ureidoglycolate.1 Publication
    Proteins known to be involved in this subpathway in this organism are:
    1. Ureidoglycolate dehydrogenase (NAD(+)) (allD)
    This subpathway is part of the pathway (S)-allantoin degradation, which is itself part of Nitrogen metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes oxalurate from (S)-ureidoglycolate, the pathway (S)-allantoin degradation and in Nitrogen metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sitei48Plays a crucial role in stabilizing the binding of (S)-ureidoglycolate1 Publication1
    Active sitei116Proton acceptor1 Publication1
    Binding sitei140NADCombined sources1 Publication1
    Binding sitei224NADCombined sources1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi174 – 176NADCombined sources1 Publication3
    Nucleotide bindingi306 – 308NADCombined sources1 Publication3

    GO - Molecular functioni

    • ureidoglycolate dehydrogenase activity Source: EcoCyc

    GO - Biological processi

    • allantoin assimilation pathway Source: EcoCyc
    • purine nucleobase metabolic process Source: UniProtKB-KW

    Keywordsi

    Molecular functionOxidoreductase
    Biological processPurine metabolism
    LigandNAD

    Enzyme and pathway databases

    BioCyciEcoCyc:G6286-MONOMER.
    MetaCyc:G6286-MONOMER.
    BRENDAi1.1.1.350. 2026.
    UniPathwayiUPA00395; UER00657.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ureidoglycolate dehydrogenase (NAD(+))1 Publication (EC:1.1.1.3501 Publication)
    Gene namesi
    Name:allD1 Publication
    Synonyms:glxB8, ylbC
    Ordered Locus Names:b0517, JW0505
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13624. allD.

    Subcellular locationi

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi43S → A: 4- and 10-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Strong decrease of the catalytic efficiency. 1 Publication1
    Mutagenesisi44H → A: 16-fold decrease of the affinity for (S)-ureidoglycolate, but same affinity for NAD compared to the wild-type. Strong decrease of the catalytic efficiency. 1 Publication1
    Mutagenesisi48R → A: Loss of dehydrogenase activity. 1 Publication1
    Mutagenesisi52Y → F: 2- and 16-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Strong decrease of the catalytic efficiency. 1 Publication1
    Mutagenesisi116H → A: Loss of dehydrogenase activity. 1 Publication1
    Mutagenesisi140S → A: 2- and 12-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Strong decrease of the catalytic efficiency. 1 Publication1
    Mutagenesisi141D → A: 5-fold decrease of the affinity for (S)-ureidoglycolate, but same affinity for NAD compared to the wild-type. Strong decrease of the catalytic efficiency. 1 Publication1
    Mutagenesisi141D → E: 14-fold decrease of the affinity for (S)-ureidoglycolate, but same affinity for NAD compared to the wild-type. Strong decrease of the catalytic efficiency. 1 Publication1
    Mutagenesisi141D → N: 6-fold decrease of the affinity for (S)-ureidoglycolate, but same affinity for NAD compared to the wild-type. Strong decrease of the catalytic efficiency. 1 Publication1
    Mutagenesisi251M → A: 2- and 13-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Slight decrease of the catalytic efficiency. 1 Publication1
    Mutagenesisi259R → A: 2- and 12-fold decrease of the affinity for NAD and (S)-ureidoglycolate, respectively. Slight decrease of the catalytic efficiency. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000838221 – 349Ureidoglycolate dehydrogenase (NAD(+))Add BLAST349

    Proteomic databases

    PaxDbiP77555.
    PRIDEiP77555.

    Expressioni

    Inductioni

    By glyoxylate and allantoin under anaerobic conditions.1 Publication

    Interactioni

    Subunit structurei

    Homodimer.1 Publication1 Publication

    Protein-protein interaction databases

    BioGridi4261441. 91 interactors.
    IntActiP77555. 5 interactors.
    STRINGi316385.ECDH10B_0473.

    Structurei

    Secondary structure

    1349
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi5 – 19Combined sources15
    Helixi23 – 39Combined sources17
    Helixi42 – 44Combined sources3
    Helixi46 – 48Combined sources3
    Helixi49 – 57Combined sources9
    Beta strandi68 – 73Combined sources6
    Beta strandi76 – 80Combined sources5
    Helixi86 – 104Combined sources19
    Beta strandi105 – 114Combined sources10
    Helixi121 – 129Combined sources9
    Beta strandi132 – 138Combined sources7
    Beta strandi149 – 151Combined sources3
    Beta strandi159 – 164Combined sources6
    Beta strandi170 – 175Combined sources6
    Beta strandi177 – 180Combined sources4
    Helixi182 – 191Combined sources10
    Beta strandi199 – 201Combined sources3
    Turni211 – 213Combined sources3
    Turni220 – 222Combined sources3
    Helixi223 – 236Combined sources14
    Helixi238 – 240Combined sources3
    Helixi245 – 247Combined sources3
    Turni251 – 253Combined sources3
    Beta strandi261 – 268Combined sources8
    Helixi270 – 272Combined sources3
    Helixi276 – 291Combined sources16
    Helixi307 – 319Combined sources13
    Beta strandi321 – 323Combined sources3
    Helixi325 – 331Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1XRHX-ray2.25A/B/C/D/E/F/G/H2-349[»]
    4H8AX-ray1.64A/B1-337[»]
    ProteinModelPortaliP77555.
    SMRiP77555.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP77555.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the LDH2/MDH2 oxidoreductase family.Curated

    Phylogenomic databases

    eggNOGiENOG4105DG4. Bacteria.
    COG2055. LUCA.
    HOGENOMiHOG000173270.
    InParanoidiP77555.
    KOiK00073.
    PhylomeDBiP77555.

    Family and domain databases

    InterProiView protein in InterPro
    IPR003767. Malate/L-lactate_DH-like.
    IPR017590. Ureidoglycolate_dehydrogenase.
    PANTHERiPTHR11091. PTHR11091. 1 hit.
    PTHR11091:SF4. PTHR11091:SF4. 1 hit.
    PfamiView protein in Pfam
    PF02615. Ldh_2. 1 hit.
    SUPFAMiSSF89733. SSF89733. 1 hit.
    TIGRFAMsiTIGR03175. AllD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P77555-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKISRETLHQ LIENKLCQAG LKREHAATVA EVLVYADARG IHSHGAVRVE
    60 70 80 90 100
    YYAERISKGG TNREPEFRLE ETGPCSAILH ADNAAGQVAA KMGMEHAIKT
    110 120 130 140 150
    AQQNGVAVVG ISRMGHSGAI SYFVQQAARA GFIGISMCQS DPMVVPFGGA
    160 170 180 190 200
    EIYYGTNPLA FAAPGEGDEI LTFDMATTVQ AWGKVLDARS RNMSIPDTWA
    210 220 230 240 250
    VDKNGVPTTD PFAVHALLPA AGPKGYGLMM MIDVLSGVLL GLPFGRQVSS
    260 270 280 290 300
    MYDDLHAGRN LGQLHIVINP NFFSSSELFR QHLSQTMREL NAITPAPGFN
    310 320 330 340
    QVYYPGQDQD IKQRKAAVEG IEIVDDIYQY LISDALYNTS YETKNPFAQ
    Length:349
    Mass (Da):37,967
    Last modified:February 1, 1997 - v1
    Checksum:i93C3076A66141C4E
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U89279 Genomic DNA. Translation: AAB93858.1.
    U82664 Genomic DNA. Translation: AAB40269.1.
    U00096 Genomic DNA. Translation: AAC73619.1.
    AP009048 Genomic DNA. Translation: BAE76295.1.
    PIRiD64783.
    RefSeqiNP_415050.1. NC_000913.3.
    WP_000703900.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC73619; AAC73619; b0517.
    BAE76295; BAE76295; BAE76295.
    GeneIDi948342.
    KEGGiecj:JW0505.
    eco:b0517.
    PATRICifig|1411691.4.peg.1761.

    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.

    Entry informationi

    Entry nameiALLD_ECOLI
    AccessioniPrimary (citable) accession number: P77555
    Secondary accession number(s): Q2MBR1
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: February 1, 1997
    Last modified: July 5, 2017
    This is version 131 of the entry and version 1 of the sequence. See 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. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families