URODH_AGRFC
ID URODH_AGRFC Reviewed; 265 AA.
AC Q7CRQ0;
DT 11-JUN-2014, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 2.
DT 03-AUG-2022, entry version 97.
DE RecName: Full=Uronate dehydrogenase;
DE EC=1.1.1.203 {ECO:0000269|PubMed:19060141, ECO:0000269|PubMed:19921179};
DE AltName: Full=D-galacturonate dehydrogenase;
DE AltName: Full=D-glucuronate dehydrogenase;
DE AltName: Full=Hexuronate dehydrogenase;
GN Name=udh; OrderedLocusNames=Atu3143;
OS Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS (strain C58)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=176299;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743193; DOI=10.1126/science.1066804;
RA Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA Gordon M.P., Olson M.V., Nester E.W.;
RT "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT C58.";
RL Science 294:2317-2323(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743194; DOI=10.1126/science.1066803;
RA Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT "Genome sequence of the plant pathogen and biotechnology agent
RT Agrobacterium tumefaciens C58.";
RL Science 294:2323-2328(2001).
RN [3]
RP IDENTIFICATION, FUNCTION, GENE NAME, CATALYTIC ACTIVITY, AND
RP BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=19060141; DOI=10.1128/jb.00586-08;
RA Yoon S.H., Moon T.S., Iranpour P., Lanza A.M., Prather K.J.;
RT "Cloning and characterization of uronate dehydrogenases from two
RT pseudomonads and Agrobacterium tumefaciens strain C58.";
RL J. Bacteriol. 191:1565-1573(2009).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY, FUNCTION, CATALYTIC ACTIVITY, KINETIC
RP PARAMETERS, SUBSTRATE SPECIFICITY, AND INDUCTION.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=19921179; DOI=10.1007/s00253-009-2333-9;
RA Boer H., Maaheimo H., Koivula A., Penttila M., Richard P.;
RT "Identification in Agrobacterium tumefaciens of the D-galacturonic acid
RT dehydrogenase gene.";
RL Appl. Microbiol. Biotechnol. 86:901-909(2010).
RN [5]
RP PATHWAY.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=24450804; DOI=10.1021/bi5000492;
RA Bouvier J.T., Groninger-Poe F.P., Vetting M., Almo S.C., Gerlt J.A.;
RT "Galactaro delta-lactone isomerase: lactone isomerization by a member of
RT the amidohydrolase superfamily.";
RL Biochemistry 53:614-616(2014).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF APOENZYME AND MUTANT ALA-134 IN
RP COMPLEXES WITH NAD AND D-GALACTARO-1,5-LACTONE, FUNCTION, IDENTIFICATION OF
RP THE REACTION PRODUCT, SUBUNIT, REACTION MECHANISM, ACTIVE SITE, AND
RP MUTAGENESIS OF TYR-134.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=21676870; DOI=10.1074/jbc.m111.254854;
RA Parkkinen T., Boer H., Janis J., Andberg M., Penttila M., Koivula A.,
RA Rouvinen J.;
RT "Crystal structure of uronate dehydrogenase from Agrobacterium
RT tumefaciens.";
RL J. Biol. Chem. 286:27294-27300(2011).
CC -!- FUNCTION: Catalyzes the oxidation of D-galacturonate and D-glucuronate
CC to galactarate and D-glucarate, respectively. In fact, in water
CC solution the substrate D-galacturonate is predominantly in pyranosic
CC form whose beta anomer is converted by the enzyme to D-galactaro-1,5-
CC lactone; in solution, this reaction product rearranges to the more
CC stable D-galactaro-1,4-lactone. Makes part of the oxidative degradation
CC pathway of D-galacturonate, which allows A.tumefaciens to utilize D-
CC galacturonate as a sole carbon source. Cannot use NADP(+) instead of
CC NAD(+) as cosubstrate. Is not active on D-galactose, D-glucose, D-
CC galactonate and D-gluconate. {ECO:0000269|PubMed:19060141,
CC ECO:0000269|PubMed:19921179, ECO:0000269|PubMed:21676870}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-D-galacturonate + NAD(+) = D-galactaro-1,5-lactone + H(+)
CC + NADH; Xref=Rhea:RHEA:22404, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:83383, ChEBI:CHEBI:85312;
CC EC=1.1.1.203; Evidence={ECO:0000269|PubMed:19060141,
CC ECO:0000269|PubMed:19921179};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=beta-D-glucuronate + NAD(+) = D-glucaro-1,5-lactone + H(+) +
CC NADH; Xref=Rhea:RHEA:43500, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:57945, ChEBI:CHEBI:83384, ChEBI:CHEBI:85313;
CC EC=1.1.1.203; Evidence={ECO:0000269|PubMed:19060141,
CC ECO:0000269|PubMed:19921179};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.37 mM for D-glucuronate {ECO:0000269|PubMed:19060141};
CC KM=1.1 mM for D-glucuronate {ECO:0000269|PubMed:19921179};
CC KM=0.16 mM for D-galacturonate {ECO:0000269|PubMed:19060141};
CC KM=0.50 mM for D-galacturonate {ECO:0000269|PubMed:19921179};
CC KM=0.18 mM for NAD(+) {ECO:0000269|PubMed:19060141};
CC KM=0.2 mM for NAD(+) {ECO:0000269|PubMed:19921179};
CC Vmax=221 umol/min/mg enzyme with D-glucuronate as substrate
CC {ECO:0000269|PubMed:19921179};
CC Vmax=124 umol/min/mg enzyme with D-galacturonate as substrate
CC {ECO:0000269|PubMed:19921179};
CC Note=kcat is 190 sec(-1) and 92 sec(-1) with D-glucuronate and D-
CC galacturonate as substrate, respectively.
CC {ECO:0000269|PubMed:19060141};
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:19060141};
CC Temperature dependence:
CC Activity increases with increasing temperatures between 4 and 42
CC degrees Celsius. Activity remains near 80% of the maximum after
CC exposure at 37 degrees Celsius for 30 minutes.
CC {ECO:0000269|PubMed:19060141};
CC -!- PATHWAY: Carbohydrate acid metabolism; D-galacturonate degradation via
CC prokaryotic oxidative pathway. {ECO:0000269|PubMed:24450804}.
CC -!- SUBUNIT: Homohexamer. {ECO:0000269|PubMed:21676870}.
CC -!- INDUCTION: By D-galacturonate. {ECO:0000269|PubMed:19921179}.
CC -!- MISCELLANEOUS: D-galactaro-1,4-lactone was previously believed to be
CC the product of the reaction of D-galacturonate oxidation.
CC {ECO:0000305|PubMed:19921179}.
CC -!- SIMILARITY: Belongs to the NAD(P)-dependent epimerase/dehydratase
CC family. {ECO:0000305}.
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DR EMBL; AE007870; AAK90243.2; -; Genomic_DNA.
DR EMBL; BK006462; DAA06454.1; -; Genomic_DNA.
DR RefSeq; NP_357458.2; NC_003063.2.
DR RefSeq; WP_010972793.1; NC_003063.2.
DR PDB; 3RFT; X-ray; 1.90 A; A/B/C=1-265.
DR PDB; 3RFV; X-ray; 2.10 A; A/B/C=1-265.
DR PDB; 3RFX; X-ray; 1.90 A; A/B/C=1-265.
DR PDBsum; 3RFT; -.
DR PDBsum; 3RFV; -.
DR PDBsum; 3RFX; -.
DR AlphaFoldDB; Q7CRQ0; -.
DR SMR; Q7CRQ0; -.
DR STRING; 176299.Atu3143; -.
DR EnsemblBacteria; AAK90243; AAK90243; Atu3143.
DR GeneID; 66223461; -.
DR KEGG; atu:Atu3143; -.
DR PATRIC; fig|176299.10.peg.2988; -.
DR eggNOG; COG0451; Bacteria.
DR HOGENOM; CLU_079334_0_0_5; -.
DR OMA; RYYFDRF; -.
DR PhylomeDB; Q7CRQ0; -.
DR BioCyc; AGRO:ATU3143-MON; -.
DR BioCyc; MetaCyc:MON-15610; -.
DR BRENDA; 1.1.1.203; 200.
DR UniPathway; UPA01050; -.
DR EvolutionaryTrace; Q7CRQ0; -.
DR Proteomes; UP000000813; Chromosome linear.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:0050388; F:uronate dehydrogenase activity; IDA:CACAO.
DR InterPro; IPR001509; Epimerase_deHydtase.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF01370; Epimerase; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
PE 1: Evidence at protein level;
KW 3D-structure; NAD; Nucleotide-binding; Oxidoreductase; Reference proteome.
FT CHAIN 1..265
FT /note="Uronate dehydrogenase"
FT /id="PRO_0000429434"
FT ACT_SITE 134
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:21676870"
FT BINDING 12..13
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 32..34
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 49..50
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 69..73
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 73
FT /ligand="substrate"
FT BINDING 109..111
FT /ligand="substrate"
FT BINDING 138
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 163
FT /ligand="substrate"
FT BINDING 164
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT BINDING 172
FT /ligand="substrate"
FT MUTAGEN 134
FT /note="Y->A: 0.1% of wild-type activity."
FT /evidence="ECO:0000269|PubMed:21676870"
FT STRAND 1..8
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 12..20
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 22..24
FT /evidence="ECO:0007829|PDB:3RFT"
FT STRAND 25..34
FT /evidence="ECO:0007829|PDB:3RFT"
FT STRAND 43..47
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 53..60
FT /evidence="ECO:0007829|PDB:3RFT"
FT STRAND 64..68
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 78..85
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 87..98
FT /evidence="ECO:0007829|PDB:3RFT"
FT STRAND 103..109
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 110..113
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 133..152
FT /evidence="ECO:0007829|PDB:3RFT"
FT STRAND 156..161
FT /evidence="ECO:0007829|PDB:3RFT"
FT STRAND 165..167
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 173..176
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 180..192
FT /evidence="ECO:0007829|PDB:3RFT"
FT STRAND 200..203
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 215..220
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 228..231
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 232..236
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 247..249
FT /evidence="ECO:0007829|PDB:3RFT"
FT HELIX 254..258
FT /evidence="ECO:0007829|PDB:3RFT"
SQ SEQUENCE 265 AA; 29047 MW; 131993C102FDF226 CRC64;
MKRLLVTGAA GQLGRVMRER LAPMAEILRL ADLSPLDPAG PNEECVQCDL ADANAVNAMV
AGCDGIVHLG GISVEKPFEQ ILQGNIIGLY NLYEAARAHG QPRIVFASSN HTIGYYPQTE
RLGPDVPARP DGLYGVSKCF GENLARMYFD KFGQETALVR IGSCTPEPNN YRMLSTWFSH
DDFVSLIEAV FRAPVLGCPV VWGASANDAG WWDNSHLGFL GWKPKDNAEA FRRHITETTP
PPDPNDALVR FQGGTFVDNP IFKQS
