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Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE (KDG aldolase YagE) (EC 4.1.2.51) (Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE) (EC 4.1.2.28)

 YAGE_ECOLI              Reviewed;         302 AA.
P75682; Q9R2D5;
01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
16-NOV-2011, sequence version 2.
28-MAR-2018, entry version 125.
RecName: Full=Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE {ECO:0000305};
Short=KDG aldolase YagE {ECO:0000305};
EC=4.1.2.51 {ECO:0000269|PubMed:21294156};
AltName: Full=Putative 2-dehydro-3-deoxy-D-pentonate aldolase YagE {ECO:0000305};
EC=4.1.2.28 {ECO:0000305|PubMed:23233208};
Name=yagE; OrderedLocusNames=b0268, JW0261;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND SEQUENCE REVISION
TO 99-100.
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-121.
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
Takemoto K., Mori H., Murayama N., Kataoka K., Yano M., Itoh T.,
Yamamoto Y., Inokuchi H., Miki T., Hatada E., Fukuda R., Ichihara S.,
Mizuno T., Makino K., Nakata A., Yura T., Sampei G., Mizobuchi K.;
"Systematic sequencing of the Escherichia coli genome: analysis of the
4.0 - 6.0 min (189,987 - 281,416bp) region.";
Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases.
[4]
FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=23233208; DOI=10.1007/s00253-012-4618-7;
Liu H., Ramos K.R., Valdehuesa K.N., Nisola G.M., Lee W.K.,
Chung W.J.;
"Biosynthesis of ethylene glycol in Escherichia coli.";
Appl. Microbiol. Biotechnol. 97:3409-3417(2013).
[5]
X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF APO-FORM, AND SUBUNIT.
PubMed=18361457; DOI=10.1002/prot.22023;
Manicka S., Peleg Y., Unger T., Albeck S., Dym O., Greenblatt H.M.,
Bourenkov G., Lamzin V., Krishnaswamy S., Sussman J.L.;
"Crystal structure of YagE, a putative DHDPS-like protein from
Escherichia coli K12.";
Proteins 71:2102-2108(2008).
[6]
X-RAY CRYSTALLOGRAPHY (2.19 ANGSTROMS) OF 5-302 IN COMPLEX WITH
PYRUVATE OR 2-KETO-3-DEOXY-GALACTONATE, FUNCTION, CATALYTIC ACTIVITY,
SUBUNIT, AND ACTIVE SITE.
PubMed=21294156; DOI=10.1002/prot.22949;
Bhaskar V., Kumar M., Manicka S., Tripathi S., Venkatraman A.,
Krishnaswamy S.;
"Identification of biochemical and putative biological role of a
xenolog from Escherichia coli using structural analysis.";
Proteins 79:1132-1142(2011).
-!- FUNCTION: Catalyzes the formation of 2-keto-3-deoxy-gluconate
(KDG) from pyruvate and glyceraldehyde (PubMed:21294156). May also
function as a 2-dehydro-3-deoxy-D-pentonate aldolase
(PubMed:23233208). Overexpression leads to increased growth (over
2 hours) in the presence of the antibiotics norfloxacin,
ampicillin and streptomycin (PubMed:21294156).
{ECO:0000269|PubMed:21294156, ECO:0000305|PubMed:23233208}.
-!- CATALYTIC ACTIVITY: 2-dehydro-3-deoxy-D-gluconate = pyruvate + D-
glyceraldehyde. {ECO:0000269|PubMed:21294156}.
-!- CATALYTIC ACTIVITY: 2-dehydro-3-deoxy-D-pentonate = pyruvate +
glycolaldehyde. {ECO:0000305|PubMed:23233208}.
-!- SUBUNIT: A dimer of dimers. {ECO:0000269|PubMed:18361457,
ECO:0000269|PubMed:21294156}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
-!- DISRUPTION PHENOTYPE: Disruption mutant has reduced ability to
catabolize D-xylonic acid. YjhH-yagE double mutant cannot use D-
xylonate as the sole source of carbon.
{ECO:0000269|PubMed:23233208}.
-!- MISCELLANEOUS: Part of prophage CP4-6.
-!- SIMILARITY: Belongs to the DapA family. {ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAA77934.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; U00096; AAC73371.2; -; Genomic_DNA.
EMBL; AP009048; BAA77934.2; ALT_INIT; Genomic_DNA.
PIR; D64752; D64752.
RefSeq; NP_414802.2; NC_000913.3.
RefSeq; WP_001136613.1; NZ_LN832404.1.
PDB; 2V8Z; X-ray; 2.20 A; A/B/C/D=1-302.
PDB; 2V9D; X-ray; 2.15 A; A/B/C/D=1-302.
PDB; 3N2X; X-ray; 2.20 A; A/B/C/D=5-302.
PDB; 3NEV; X-ray; 2.19 A; A/B/C/D=5-302.
PDB; 4OE7; X-ray; 1.99 A; A/B/C/D=1-302.
PDB; 4ONV; X-ray; 2.57 A; A/B/C/D=1-302.
PDB; 4PTN; X-ray; 1.99 A; A/B/C/D=1-302.
PDB; 4U4M; X-ray; 3.09 A; A/B/C/D=5-302.
PDBsum; 2V8Z; -.
PDBsum; 2V9D; -.
PDBsum; 3N2X; -.
PDBsum; 3NEV; -.
PDBsum; 4OE7; -.
PDBsum; 4ONV; -.
PDBsum; 4PTN; -.
PDBsum; 4U4M; -.
ProteinModelPortal; P75682; -.
SMR; P75682; -.
BioGrid; 4261826; 7.
DIP; DIP-11232N; -.
IntAct; P75682; 3.
STRING; 316385.ECDH10B_0255; -.
PaxDb; P75682; -.
PRIDE; P75682; -.
EnsemblBacteria; AAC73371; AAC73371; b0268.
EnsemblBacteria; BAA77934; BAA77934; BAA77934.
GeneID; 944925; -.
KEGG; ecj:JW0261; -.
KEGG; eco:b0268; -.
PATRIC; fig|1411691.4.peg.2012; -.
EchoBASE; EB3128; -.
EcoGene; EG13344; yagE.
eggNOG; ENOG4105CDP; Bacteria.
eggNOG; COG0329; LUCA.
HOGENOM; HOG000173604; -.
InParanoid; P75682; -.
KO; K22397; -.
BioCyc; EcoCyc:G6140-MONOMER; -.
BioCyc; MetaCyc:G6140-MONOMER; -.
BRENDA; 4.1.2.20; 2026.
EvolutionaryTrace; P75682; -.
PRO; PR:P75682; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0061677; F:2-dehydro-3-deoxy-D-gluconate aldolase activity; IEA:UniProtKB-EC.
GO; GO:0047440; F:2-dehydro-3-deoxy-D-pentonate aldolase activity; IEA:UniProtKB-EC.
GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
GO; GO:0046176; P:aldonic acid catabolic process; IMP:EcoCyc.
Gene3D; 3.20.20.70; -; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR002220; DapA-like.
InterPro; IPR020625; Schiff_base-form_aldolases_AS.
InterPro; IPR020624; Schiff_base-form_aldolases_CS.
PANTHER; PTHR12128; PTHR12128; 1.
Pfam; PF00701; DHDPS; 1.
PIRSF; PIRSF001365; DHDPS; 1.
PRINTS; PR00146; DHPICSNTHASE.
SMART; SM01130; DHDPS; 1.
PROSITE; PS00665; DHDPS_1; 1.
PROSITE; PS00666; DHDPS_2; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Cytoplasm; Lyase; Reference proteome;
Schiff base.
CHAIN 1 302 Putative 2-dehydro-3-deoxy-D-gluconate
aldolase YagE.
/FTId=PRO_0000103244.
ACT_SITE 49 49 Charge relay system.
{ECO:0000305|PubMed:21294156}.
ACT_SITE 112 112 Charge relay system.
{ECO:0000305|PubMed:21294156}.
ACT_SITE 138 138 Proton donor.
{ECO:0000305|PubMed:21294156}.
ACT_SITE 167 167 Schiff-base intermediate with substrate.
{ECO:0000305|PubMed:21294156}.
STRAND 22 24 {ECO:0000244|PDB:2V9D}.
HELIX 26 38 {ECO:0000244|PDB:4OE7}.
STRAND 44 48 {ECO:0000244|PDB:4OE7}.
HELIX 49 51 {ECO:0000244|PDB:4OE7}.
HELIX 53 55 {ECO:0000244|PDB:4OE7}.
HELIX 58 72 {ECO:0000244|PDB:4OE7}.
STRAND 78 81 {ECO:0000244|PDB:4OE7}.
HELIX 87 99 {ECO:0000244|PDB:4OE7}.
STRAND 103 108 {ECO:0000244|PDB:4OE7}.
STRAND 111 113 {ECO:0000244|PDB:4OE7}.
HELIX 117 129 {ECO:0000244|PDB:4OE7}.
STRAND 135 139 {ECO:0000244|PDB:4OE7}.
HELIX 141 144 {ECO:0000244|PDB:4OE7}.
HELIX 150 159 {ECO:0000244|PDB:4OE7}.
STRAND 163 168 {ECO:0000244|PDB:4OE7}.
HELIX 173 186 {ECO:0000244|PDB:4OE7}.
STRAND 191 196 {ECO:0000244|PDB:4OE7}.
HELIX 197 199 {ECO:0000244|PDB:4OE7}.
HELIX 200 205 {ECO:0000244|PDB:4OE7}.
HELIX 214 216 {ECO:0000244|PDB:4OE7}.
HELIX 220 232 {ECO:0000244|PDB:4OE7}.
HELIX 235 247 {ECO:0000244|PDB:4OE7}.
HELIX 248 254 {ECO:0000244|PDB:4OE7}.
STRAND 255 257 {ECO:0000244|PDB:4OE7}.
HELIX 259 268 {ECO:0000244|PDB:4OE7}.
HELIX 286 298 {ECO:0000244|PDB:4OE7}.
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


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