YAGE_ECOLI
ID YAGE_ECOLI Reviewed; 302 AA.
AC P75682; Q9R2D5;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 16-NOV-2011, sequence version 2.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE {ECO:0000305};
DE Short=KDG aldolase YagE {ECO:0000305};
DE EC=4.1.2.51 {ECO:0000269|PubMed:21294156};
DE AltName: Full=Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE {ECO:0000305};
DE EC=4.1.2.28 {ECO:0000305|PubMed:23233208};
GN Name=yagE; OrderedLocusNames=b0268, JW0261;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION TO
RP 99-100.
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-121.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T.,
RA Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S.,
RA Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.;
RT "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0
RT - 6.0 min (189,987 - 281,416bp) region.";
RL Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=23233208; DOI=10.1007/s00253-012-4618-7;
RA Liu H., Ramos K.R., Valdehuesa K.N., Nisola G.M., Lee W.K., Chung W.J.;
RT "Biosynthesis of ethylene glycol in Escherichia coli.";
RL Appl. Microbiol. Biotechnol. 97:3409-3417(2013).
RN [5]
RP INDUCTION.
RX PubMed=29087459; DOI=10.1093/femsle/fnx220;
RA Shimada T., Momiyama E., Yamanaka Y., Watanabe H., Yamamoto K.,
RA Ishihama A.;
RT "Regulatory role of XynR (YagI) in catabolism of xylonate in Escherichia
RT coli K-12.";
RL FEMS Microbiol. Lett. 364:0-0(2017).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF APO-FORM, AND SUBUNIT.
RX PubMed=18361457; DOI=10.1002/prot.22023;
RA Manicka S., Peleg Y., Unger T., Albeck S., Dym O., Greenblatt H.M.,
RA Bourenkov G., Lamzin V., Krishnaswamy S., Sussman J.L.;
RT "Crystal structure of YagE, a putative DHDPS-like protein from Escherichia
RT coli K12.";
RL Proteins 71:2102-2108(2008).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.19 ANGSTROMS) OF 5-302 IN COMPLEX WITH PYRUVATE OR
RP 2-KETO-3-DEOXY-GALACTONATE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT, AND
RP ACTIVE SITE.
RX PubMed=21294156; DOI=10.1002/prot.22949;
RA Bhaskar V., Kumar M., Manicka S., Tripathi S., Venkatraman A.,
RA Krishnaswamy S.;
RT "Identification of biochemical and putative biological role of a xenolog
RT from Escherichia coli using structural analysis.";
RL Proteins 79:1132-1142(2011).
CC -!- FUNCTION: Catalyzes the formation of 2-keto-3-deoxy-gluconate (KDG)
CC from pyruvate and glyceraldehyde (PubMed:21294156). May also function
CC as a 2-dehydro-3-deoxy-D-pentonate aldolase (PubMed:23233208).
CC Overexpression leads to increased growth (over 2 hours) in the presence
CC of the antibiotics norfloxacin, ampicillin and streptomycin
CC (PubMed:21294156). {ECO:0000269|PubMed:21294156,
CC ECO:0000305|PubMed:23233208}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-dehydro-3-deoxy-D-gluconate = D-glyceraldehyde + pyruvate;
CC Xref=Rhea:RHEA:35583, ChEBI:CHEBI:15361, ChEBI:CHEBI:17378,
CC ChEBI:CHEBI:57990; EC=4.1.2.51;
CC Evidence={ECO:0000269|PubMed:21294156};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-dehydro-3-deoxy-D-arabinonate = glycolaldehyde + pyruvate;
CC Xref=Rhea:RHEA:20609, ChEBI:CHEBI:15361, ChEBI:CHEBI:16699,
CC ChEBI:CHEBI:17071; EC=4.1.2.28;
CC Evidence={ECO:0000305|PubMed:23233208};
CC -!- SUBUNIT: A dimer of dimers. {ECO:0000269|PubMed:18361457,
CC ECO:0000269|PubMed:21294156}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- INDUCTION: Expression is repressed by the transcriptional regulator
CC XynR. {ECO:0000269|PubMed:29087459}.
CC -!- DISRUPTION PHENOTYPE: Disruption mutant has reduced ability to
CC catabolize D-xylonic acid. YjhH-yagE double mutant cannot use D-
CC xylonate as the sole source of carbon. {ECO:0000269|PubMed:23233208}.
CC -!- MISCELLANEOUS: Part of prophage CP4-6.
CC -!- SIMILARITY: Belongs to the DapA family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA77934.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC73371.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA77934.2; ALT_INIT; Genomic_DNA.
DR PIR; D64752; D64752.
DR RefSeq; NP_414802.2; NC_000913.3.
DR RefSeq; WP_001136613.1; NZ_LN832404.1.
DR PDB; 2V8Z; X-ray; 2.20 A; A/B/C/D=1-302.
DR PDB; 2V9D; X-ray; 2.15 A; A/B/C/D=1-302.
DR PDB; 3N2X; X-ray; 2.20 A; A/B/C/D=5-302.
DR PDB; 3NEV; X-ray; 2.19 A; A/B/C/D=5-302.
DR PDB; 4OE7; X-ray; 1.99 A; A/B/C/D=1-302.
DR PDB; 4ONV; X-ray; 2.57 A; A/B/C/D=1-302.
DR PDB; 4PTN; X-ray; 1.99 A; A/B/C/D=1-302.
DR PDB; 4U4M; X-ray; 3.09 A; A/B/C/D=5-302.
DR PDBsum; 2V8Z; -.
DR PDBsum; 2V9D; -.
DR PDBsum; 3N2X; -.
DR PDBsum; 3NEV; -.
DR PDBsum; 4OE7; -.
DR PDBsum; 4ONV; -.
DR PDBsum; 4PTN; -.
DR PDBsum; 4U4M; -.
DR AlphaFoldDB; P75682; -.
DR SMR; P75682; -.
DR BioGRID; 4261826; 7.
DR DIP; DIP-11232N; -.
DR IntAct; P75682; 3.
DR STRING; 511145.b0268; -.
DR jPOST; P75682; -.
DR PaxDb; P75682; -.
DR PRIDE; P75682; -.
DR EnsemblBacteria; AAC73371; AAC73371; b0268.
DR EnsemblBacteria; BAA77934; BAA77934; BAA77934.
DR GeneID; 944925; -.
DR KEGG; ecj:JW0261; -.
DR KEGG; eco:b0268; -.
DR PATRIC; fig|1411691.4.peg.2012; -.
DR EchoBASE; EB3128; -.
DR eggNOG; COG0329; Bacteria.
DR HOGENOM; CLU_049343_5_1_6; -.
DR InParanoid; P75682; -.
DR OMA; VVPPVCT; -.
DR PhylomeDB; P75682; -.
DR BioCyc; EcoCyc:G6140-MON; -.
DR BioCyc; MetaCyc:G6140-MON; -.
DR BRENDA; 4.1.2.20; 2026.
DR EvolutionaryTrace; P75682; -.
DR PRO; PR:P75682; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0061677; F:2-dehydro-3-deoxy-D-gluconate aldolase activity; IEA:UniProtKB-EC.
DR GO; GO:0047440; F:2-dehydro-3-deoxy-D-pentonate aldolase activity; IEA:UniProtKB-EC.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0046176; P:aldonic acid catabolic process; IMP:EcoCyc.
DR Gene3D; 3.20.20.70; -; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR002220; DapA-like.
DR InterPro; IPR020625; Schiff_base-form_aldolases_AS.
DR InterPro; IPR020624; Schiff_base-form_aldolases_CS.
DR PANTHER; PTHR12128; PTHR12128; 1.
DR Pfam; PF00701; DHDPS; 1.
DR PIRSF; PIRSF001365; DHDPS; 1.
DR PRINTS; PR00146; DHPICSNTHASE.
DR SMART; SM01130; DHDPS; 1.
DR PROSITE; PS00665; DHDPS_1; 1.
DR PROSITE; PS00666; DHDPS_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Lyase; Reference proteome; Schiff base.
FT CHAIN 1..302
FT /note="Putative 2-dehydro-3-deoxy-D-gluconate aldolase
FT YagE"
FT /id="PRO_0000103244"
FT ACT_SITE 49
FT /note="Charge relay system"
FT /evidence="ECO:0000305|PubMed:21294156"
FT ACT_SITE 112
FT /note="Charge relay system"
FT /evidence="ECO:0000305|PubMed:21294156"
FT ACT_SITE 138
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:21294156"
FT ACT_SITE 167
FT /note="Schiff-base intermediate with substrate"
FT /evidence="ECO:0000305|PubMed:21294156"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:2V9D"
FT HELIX 26..38
FT /evidence="ECO:0007829|PDB:4OE7"
FT STRAND 44..48
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 53..55
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 58..72
FT /evidence="ECO:0007829|PDB:4OE7"
FT STRAND 78..81
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 87..99
FT /evidence="ECO:0007829|PDB:4OE7"
FT STRAND 103..108
FT /evidence="ECO:0007829|PDB:4OE7"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 117..129
FT /evidence="ECO:0007829|PDB:4OE7"
FT STRAND 135..139
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 141..144
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 150..159
FT /evidence="ECO:0007829|PDB:4OE7"
FT STRAND 163..168
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 173..186
FT /evidence="ECO:0007829|PDB:4OE7"
FT STRAND 191..196
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 197..199
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 200..205
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 214..216
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 220..232
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 235..247
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 248..254
FT /evidence="ECO:0007829|PDB:4OE7"
FT STRAND 255..257
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 259..268
FT /evidence="ECO:0007829|PDB:4OE7"
FT HELIX 286..298
FT /evidence="ECO:0007829|PDB:4OE7"
SQ SEQUENCE 302 AA; 32530 MW; 3ED5545FA2D739BA CRC64;
MPQSALFTGI IPPVSTIFTA DGQLDKPGTA ALIDDLIKAG VDGLFFLGSG GEFSQLGAEE
RKAIARFAID HVDRRVPVLI GTGGTNARET IELSQHAQQA GADGIVVINP YYWKVSEANL
IRYFEQVADS VTLPVMLYNF PALTGQDLTP ALVKTLADSR SNIIGIKDTI DSVAHLRSMI
HTVKGAHPHF TVLCGYDDHL FNTLLLGGDG AISASGNFAP QVSVNLLKAW RDGDVAKAAG
YHQTLLQIPQ MYQLDTPFVN VIKEAIVLCG RPVSTHVLPP ASPLDEPRKA QLKTLLQQLK
LC
