ALLD_ECOLI
ID ALLD_ECOLI Reviewed; 349 AA.
AC P77555; Q2MBR1;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 152.
DE RecName: Full=Ureidoglycolate dehydrogenase (NAD(+)) {ECO:0000303|PubMed:23284870};
DE EC=1.1.1.350 {ECO:0000269|PubMed:23284870};
GN Name=allD {ECO:0000303|PubMed:10601204}; Synonyms=glxB8, ylbC;
GN OrderedLocusNames=b0517, JW0505;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, PATHWAY, AND INDUCTION.
RC STRAIN=K12 / ECL1;
RX PubMed=10601204; DOI=10.1128/jb.181.24.7479-7484.1999;
RA Cusa E., Obradors N., Baldoma L., Badia J., Aguilar J.;
RT "Genetic analysis of a chromosomal region containing genes required for
RT assimilation of allantoin nitrogen and linked glyoxylate metabolism in
RT Escherichia coli.";
RL J. Bacteriol. 181:7479-7484(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF 2-349, AND SUBUNIT.
RA Rajashankar K.R., Kniewel R., Lima C.D.;
RT "Crystal structure of ureidoglycolate dehydrogenase from Escherichia
RT coli.";
RL Submitted (OCT-2004) to the PDB data bank.
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.64 ANGSTROMS) OF 1-337 IN COMPLEX WITH NAD,
RP FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF SER-43; HIS-44; ARG-48;
RP TYR-52; HIS-116; SER-140; ASP-141; MET-251 AND ARG-259, SUBUNIT, ACTIVE
RP SITE, AND REACTION MECHANISM.
RX PubMed=23284870; DOI=10.1371/journal.pone.0052066;
RA Kim M.I., Shin I., Cho S., Lee J., Rhee S.;
RT "Structural and functional insights into (S)-ureidoglycolate dehydrogenase,
RT a metabolic branch point enzyme in nitrogen utilization.";
RL PLoS ONE 7:E52066-E52066(2012).
CC -!- FUNCTION: AllD plays a pivotal role as a metabolic branch-point enzyme
CC in nitrogen utilization via the assimilation of allantoin
CC (PubMed:10601204). It is able to utilize allantoin as a sole source of
CC nitrogen under anaerobic conditions (PubMed:10601204). Catalyzes the
CC oxidation of ureidoglycolate to oxalurate (PubMed:23284870).
CC {ECO:0000269|PubMed:10601204, ECO:0000269|PubMed:23284870}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-ureidoglycolate + NAD(+) = H(+) + N-carbamoyl-2-oxoglycine
CC + NADH; Xref=Rhea:RHEA:15329, ChEBI:CHEBI:15378, ChEBI:CHEBI:57296,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:57824, ChEBI:CHEBI:57945;
CC EC=1.1.1.350; Evidence={ECO:0000269|PubMed:23284870};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.56 mM for NAD {ECO:0000269|PubMed:23284870};
CC KM=1.06 mM for (S)-ureidoglycolate {ECO:0000269|PubMed:23284870};
CC Note=Kact is 62.39 sec(-1) for dehydrogenase activity with NAD. Kact
CC is 57.06 sec(-1) for dehydrogenase activity with (S)-ureidoglycolate.
CC {ECO:0000269|PubMed:23284870};
CC -!- PATHWAY: Nitrogen metabolism; (S)-allantoin degradation; oxalurate from
CC (S)-ureidoglycolate: step 1/1. {ECO:0000305|PubMed:10601204}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:23284870, ECO:0000305|Ref.5}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: By glyoxylate and allantoin under anaerobic conditions.
CC {ECO:0000269|PubMed:10601204}.
CC -!- SIMILARITY: Belongs to the LDH2/MDH2 oxidoreductase family.
CC {ECO:0000305}.
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DR EMBL; U89279; AAB93858.1; -; Genomic_DNA.
DR EMBL; U82664; AAB40269.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73619.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76295.1; -; Genomic_DNA.
DR PIR; D64783; D64783.
DR RefSeq; NP_415050.1; NC_000913.3.
DR RefSeq; WP_000703900.1; NZ_SSZK01000024.1.
DR PDB; 1XRH; X-ray; 2.25 A; A/B/C/D/E/F/G/H=2-349.
DR PDB; 4H8A; X-ray; 1.64 A; A/B=1-337.
DR PDBsum; 1XRH; -.
DR PDBsum; 4H8A; -.
DR AlphaFoldDB; P77555; -.
DR SMR; P77555; -.
DR BioGRID; 4261441; 91.
DR IntAct; P77555; 5.
DR STRING; 511145.b0517; -.
DR PaxDb; P77555; -.
DR PRIDE; P77555; -.
DR DNASU; 948342; -.
DR EnsemblBacteria; AAC73619; AAC73619; b0517.
DR EnsemblBacteria; BAE76295; BAE76295; BAE76295.
DR GeneID; 948342; -.
DR KEGG; ecj:JW0505; -.
DR KEGG; eco:b0517; -.
DR PATRIC; fig|1411691.4.peg.1761; -.
DR EchoBASE; EB3389; -.
DR eggNOG; COG2055; Bacteria.
DR HOGENOM; CLU_040452_3_1_6; -.
DR InParanoid; P77555; -.
DR OMA; CSDYRGH; -.
DR PhylomeDB; P77555; -.
DR BioCyc; EcoCyc:G6286-MON; -.
DR BioCyc; MetaCyc:G6286-MON; -.
DR BRENDA; 1.1.1.350; 2026.
DR UniPathway; UPA00395; UER00657.
DR EvolutionaryTrace; P77555; -.
DR PRO; PR:P77555; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0009040; F:ureidoglycolate dehydrogenase activity; IDA:EcoCyc.
DR GO; GO:0009442; P:allantoin assimilation pathway; IDA:EcoCyc.
DR GO; GO:0006144; P:purine nucleobase metabolic process; IEA:UniProtKB-KW.
DR Gene3D; 1.10.1530.10; -; 1.
DR Gene3D; 3.30.1370.60; -; 1.
DR InterPro; IPR043144; Mal/L-sulf/L-lact_DH-like_ah.
DR InterPro; IPR043143; Mal/L-sulf/L-lact_DH-like_NADP.
DR InterPro; IPR036111; Mal/L-sulfo/L-lacto_DH-like_sf.
DR InterPro; IPR003767; Malate/L-lactate_DH-like.
DR InterPro; IPR017590; Ureidoglycolate_dehydrogenase.
DR PANTHER; PTHR11091; PTHR11091; 1.
DR Pfam; PF02615; Ldh_2; 1.
DR SUPFAM; SSF89733; SSF89733; 1.
DR TIGRFAMs; TIGR03175; AllD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; NAD; Oxidoreductase; Purine metabolism;
KW Reference proteome.
FT CHAIN 1..349
FT /note="Ureidoglycolate dehydrogenase (NAD(+))"
FT /id="PRO_0000083822"
FT ACT_SITE 116
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:23284870"
FT BINDING 140
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000305|PubMed:23284870,
FT ECO:0007744|PDB:4H8A"
FT BINDING 174..176
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000305|PubMed:23284870,
FT ECO:0007744|PDB:4H8A"
FT BINDING 224
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000305|PubMed:23284870,
FT ECO:0007744|PDB:4H8A"
FT BINDING 306..308
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000305|PubMed:23284870,
FT ECO:0007744|PDB:4H8A"
FT SITE 48
FT /note="Plays a crucial role in stabilizing the binding of
FT (S)-ureidoglycolate"
FT /evidence="ECO:0000305|PubMed:23284870"
FT MUTAGEN 43
FT /note="S->A: 4- and 10-fold decrease of the affinity for
FT NAD and (S)-ureidoglycolate, respectively. Strong decrease
FT of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 44
FT /note="H->A: 16-fold decrease of the affinity for (S)-
FT ureidoglycolate, but same affinity for NAD compared to the
FT wild-type. Strong decrease of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 48
FT /note="R->A: Loss of dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 52
FT /note="Y->F: 2- and 16-fold decrease of the affinity for
FT NAD and (S)-ureidoglycolate, respectively. Strong decrease
FT of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 116
FT /note="H->A: Loss of dehydrogenase activity."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 140
FT /note="S->A: 2- and 12-fold decrease of the affinity for
FT NAD and (S)-ureidoglycolate, respectively. Strong decrease
FT of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 141
FT /note="D->A: 5-fold decrease of the affinity for (S)-
FT ureidoglycolate, but same affinity for NAD compared to the
FT wild-type. Strong decrease of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 141
FT /note="D->E: 14-fold decrease of the affinity for (S)-
FT ureidoglycolate, but same affinity for NAD compared to the
FT wild-type. Strong decrease of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 141
FT /note="D->N: 6-fold decrease of the affinity for (S)-
FT ureidoglycolate, but same affinity for NAD compared to the
FT wild-type. Strong decrease of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 251
FT /note="M->A: 2- and 13-fold decrease of the affinity for
FT NAD and (S)-ureidoglycolate, respectively. Slight decrease
FT of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT MUTAGEN 259
FT /note="R->A: 2- and 12-fold decrease of the affinity for
FT NAD and (S)-ureidoglycolate, respectively. Slight decrease
FT of the catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:23284870"
FT HELIX 5..19
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 23..39
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 42..44
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 46..48
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 49..57
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 68..73
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 76..80
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 86..104
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 105..114
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 121..129
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 132..138
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 149..151
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 170..175
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 177..180
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 182..191
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:4H8A"
FT TURN 211..213
FT /evidence="ECO:0007829|PDB:1XRH"
FT TURN 220..222
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 223..236
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 238..240
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 245..247
FT /evidence="ECO:0007829|PDB:4H8A"
FT TURN 251..253
FT /evidence="ECO:0007829|PDB:1XRH"
FT STRAND 261..268
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 270..272
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 276..291
FT /evidence="ECO:0007829|PDB:4H8A"
FT HELIX 307..319
FT /evidence="ECO:0007829|PDB:4H8A"
FT STRAND 321..323
FT /evidence="ECO:0007829|PDB:1XRH"
FT HELIX 325..331
FT /evidence="ECO:0007829|PDB:4H8A"
SQ SEQUENCE 349 AA; 37967 MW; 93C3076A66141C4E CRC64;
MKISRETLHQ LIENKLCQAG LKREHAATVA EVLVYADARG IHSHGAVRVE YYAERISKGG
TNREPEFRLE ETGPCSAILH ADNAAGQVAA KMGMEHAIKT AQQNGVAVVG ISRMGHSGAI
SYFVQQAARA GFIGISMCQS DPMVVPFGGA EIYYGTNPLA FAAPGEGDEI LTFDMATTVQ
AWGKVLDARS RNMSIPDTWA VDKNGVPTTD PFAVHALLPA AGPKGYGLMM MIDVLSGVLL
GLPFGRQVSS MYDDLHAGRN LGQLHIVINP NFFSSSELFR QHLSQTMREL NAITPAPGFN
QVYYPGQDQD IKQRKAAVEG IEIVDDIYQY LISDALYNTS YETKNPFAQ
