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Protein

Probable 2-keto-3-deoxy-galactonate aldolase YagE

Gene

yagE

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the formation of 2-keto-3-deoxy-galactonate (KDGal) from pyruvate and glyceraldehyde. Overexpression leads to increased growth (over 2 hours) in the presence of the antibiotics norfloxacin, ampicillin and streptomycin.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei49 – 491Charge relay systemCurated
Active sitei112 – 1121Charge relay systemCurated
Active sitei138 – 1381Proton donorCurated
Active sitei167 – 1671Schiff-base intermediate with substrate

GO - Molecular functioni

  • identical protein binding Source: EcoCyc
  • lyase activity Source: UniProtKB-KW

GO - Biological processi

  • aldonic acid catabolic process Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Schiff base

Enzyme and pathway databases

BioCyciEcoCyc:G6140-MONOMER.
ECOL316407:JW0261-MONOMER.
MetaCyc:G6140-MONOMER.
BRENDAi4.1.2.20. 2026.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable 2-keto-3-deoxy-galactonate aldolase YagE (EC:4.1.2.-)
Short name:
Probable KDGal aldolase YagE
Gene namesi
Name:yagE
Ordered Locus Names:b0268, JW0261
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13344. yagE.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 302302Probable 2-keto-3-deoxy-galactonate aldolase YagEPRO_0000103244Add
BLAST

Proteomic databases

EPDiP75682.
PaxDbiP75682.

Interactioni

Subunit structurei

A dimer of dimers.2 Publications

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4261826. 7 interactions.
DIPiDIP-11232N.
IntActiP75682. 3 interactions.
STRINGi511145.b0268.

Structurei

Secondary structure

1
302
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi22 – 243Combined sources
Helixi26 – 3813Combined sources
Beta strandi44 – 485Combined sources
Helixi49 – 513Combined sources
Helixi53 – 553Combined sources
Helixi58 – 7215Combined sources
Beta strandi78 – 814Combined sources
Helixi87 – 9913Combined sources
Beta strandi103 – 1086Combined sources
Beta strandi111 – 1133Combined sources
Helixi117 – 12913Combined sources
Beta strandi135 – 1395Combined sources
Helixi141 – 1444Combined sources
Helixi150 – 15910Combined sources
Beta strandi163 – 1686Combined sources
Helixi173 – 18614Combined sources
Beta strandi191 – 1966Combined sources
Helixi197 – 1993Combined sources
Helixi200 – 2056Combined sources
Helixi214 – 2163Combined sources
Helixi220 – 23213Combined sources
Helixi235 – 24713Combined sources
Helixi248 – 2547Combined sources
Beta strandi255 – 2573Combined sources
Helixi259 – 26810Combined sources
Helixi286 – 29813Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2V8ZX-ray2.20A/B/C/D1-302[»]
2V9DX-ray2.15A/B/C/D1-302[»]
3N2XX-ray2.20A/B/C/D5-302[»]
3NEVX-ray2.19A/B/C/D5-302[»]
4OE7X-ray1.99A/B/C/D1-302[»]
4ONVX-ray2.57A/B/C/D1-302[»]
4PTNX-ray1.99A/B/C/D1-302[»]
4U4MX-ray3.09A/B/C/D5-302[»]
ProteinModelPortaliP75682.
SMRiP75682. Positions 5-290.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP75682.

Family & Domainsi

Sequence similaritiesi

Belongs to the DapA family.Curated

Phylogenomic databases

eggNOGiENOG4105CDP. Bacteria.
COG0329. LUCA.
HOGENOMiHOG000173604.
InParanoidiP75682.
KOiK01714.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR002220. DapA-like.
IPR020625. Schiff_base-form_aldolases_AS.
IPR020624. Schiff_base-form_aldolases_CS.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PIRSFiPIRSF001365. DHDPS. 1 hit.
PRINTSiPR00146. DHPICSNTHASE.
SMARTiSM01130. DHDPS. 1 hit.
[Graphical view]
PROSITEiPS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P75682-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPQSALFTGI IPPVSTIFTA DGQLDKPGTA ALIDDLIKAG VDGLFFLGSG
60 70 80 90 100
GEFSQLGAEE RKAIARFAID HVDRRVPVLI GTGGTNARET IELSQHAQQA
110 120 130 140 150
GADGIVVINP YYWKVSEANL IRYFEQVADS VTLPVMLYNF PALTGQDLTP
160 170 180 190 200
ALVKTLADSR SNIIGIKDTI DSVAHLRSMI HTVKGAHPHF TVLCGYDDHL
210 220 230 240 250
FNTLLLGGDG AISASGNFAP QVSVNLLKAW RDGDVAKAAG YHQTLLQIPQ
260 270 280 290 300
MYQLDTPFVN VIKEAIVLCG RPVSTHVLPP ASPLDEPRKA QLKTLLQQLK

LC
Length:302
Mass (Da):32,530
Last modified:November 16, 2011 - v2
Checksum:i3ED5545FA2D739BA
GO

Sequence cautioni

The sequence BAA77934.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73371.2.
AP009048 Genomic DNA. Translation: BAA77934.2. Different initiation.
PIRiD64752.
RefSeqiNP_414802.2. NC_000913.3.
WP_001136613.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73371; AAC73371; b0268.
BAA77934; BAA77934; BAA77934.
GeneIDi944925.
KEGGiecj:JW0261.
eco:b0268.
PATRICi32115657. VBIEscCol129921_0272.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC73371.2.
AP009048 Genomic DNA. Translation: BAA77934.2. Different initiation.
PIRiD64752.
RefSeqiNP_414802.2. NC_000913.3.
WP_001136613.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2V8ZX-ray2.20A/B/C/D1-302[»]
2V9DX-ray2.15A/B/C/D1-302[»]
3N2XX-ray2.20A/B/C/D5-302[»]
3NEVX-ray2.19A/B/C/D5-302[»]
4OE7X-ray1.99A/B/C/D1-302[»]
4ONVX-ray2.57A/B/C/D1-302[»]
4PTNX-ray1.99A/B/C/D1-302[»]
4U4MX-ray3.09A/B/C/D5-302[»]
ProteinModelPortaliP75682.
SMRiP75682. Positions 5-290.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4261826. 7 interactions.
DIPiDIP-11232N.
IntActiP75682. 3 interactions.
STRINGi511145.b0268.

Proteomic databases

EPDiP75682.
PaxDbiP75682.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73371; AAC73371; b0268.
BAA77934; BAA77934; BAA77934.
GeneIDi944925.
KEGGiecj:JW0261.
eco:b0268.
PATRICi32115657. VBIEscCol129921_0272.

Organism-specific databases

EchoBASEiEB3128.
EcoGeneiEG13344. yagE.

Phylogenomic databases

eggNOGiENOG4105CDP. Bacteria.
COG0329. LUCA.
HOGENOMiHOG000173604.
InParanoidiP75682.
KOiK01714.

Enzyme and pathway databases

BioCyciEcoCyc:G6140-MONOMER.
ECOL316407:JW0261-MONOMER.
MetaCyc:G6140-MONOMER.
BRENDAi4.1.2.20. 2026.

Miscellaneous databases

EvolutionaryTraceiP75682.
PROiP75682.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
InterProiIPR013785. Aldolase_TIM.
IPR002220. DapA-like.
IPR020625. Schiff_base-form_aldolases_AS.
IPR020624. Schiff_base-form_aldolases_CS.
[Graphical view]
PANTHERiPTHR12128. PTHR12128. 1 hit.
PfamiPF00701. DHDPS. 1 hit.
[Graphical view]
PIRSFiPIRSF001365. DHDPS. 1 hit.
PRINTSiPR00146. DHPICSNTHASE.
SMARTiSM01130. DHDPS. 1 hit.
[Graphical view]
PROSITEiPS00665. DHDPS_1. 1 hit.
PS00666. DHDPS_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  2. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], SEQUENCE REVISION TO 99-100.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. "Systematic sequencing of the Escherichia coli genome: analysis of the 4.0 - 6.0 min (189,987 - 281,416bp) region."
    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.
    Submitted (FEB-1996) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] OF 1-121.
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12."
    Manicka S., Peleg Y., Unger T., Albeck S., Dym O., Greenblatt H.M., Bourenkov G., Lamzin V., Krishnaswamy S., Sussman J.L.
    Proteins 71:2102-2108(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF APO-FORM, SUBUNIT.
  5. "Identification of biochemical and putative biological role of a xenolog from Escherichia coli using structural analysis."
    Bhaskar V., Kumar M., Manicka S., Tripathi S., Venkatraman A., Krishnaswamy S.
    Proteins 79:1132-1142(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.19 ANGSTROMS) OF 5-302 IN COMPLEX WITH PYRUVATE OR 2-KETO-3-DEOXY-GALACTONATE.

Entry informationi

Entry nameiYAGE_ECOLI
AccessioniPrimary (citable) accession number: P75682
Secondary accession number(s): Q9R2D5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 16, 2011
Last modified: May 11, 2016
This is version 116 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

Part of prophage CP4-6.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

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.