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Protein

Deoxyribose-phosphate aldolase

Gene

deoC

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

Functioni

Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.

Catalytic activityi

2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde.

Pathway: 2-deoxy-D-ribose 1-phosphate degradation

This protein is involved in step 2 of the subpathway that synthesizes D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate.
Proteins known to be involved in the 2 steps of the subpathway in this organism are:
  1. no protein annotated in this organism
  2. Deoxyribose-phosphate aldolase (deoC), Deoxyribose-phosphate aldolase (deoC)
This subpathway is part of the pathway 2-deoxy-D-ribose 1-phosphate degradation, which is itself part of Carbohydrate degradation.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-alpha-D-ribose 1-phosphate, the pathway 2-deoxy-D-ribose 1-phosphate degradation and in Carbohydrate degradation.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei167 – 1671Schiff-base intermediate with acetaldehyde1 Publication
Active sitei201 – 20111 Publication

GO - Molecular functioni

  • deoxyribose-phosphate aldolase activity Source: EcoCyc
  • lyase activity Source: EcoliWiki

GO - Biological processi

  • carbohydrate catabolic process Source: EcoliWiki
  • cellular response to DNA damage stimulus Source: EcoliWiki
  • deoxyribonucleotide catabolic process Source: EcoliWiki
  • deoxyribose phosphate catabolic process Source: UniProtKB-UniPathway
  • nucleobase-containing small molecule interconversion Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Schiff base

Enzyme and pathway databases

BioCyciEcoCyc:DEOXYRIBOSE-P-ALD-MONOMER.
ECOL316407:JW4344-MONOMER.
MetaCyc:DEOXYRIBOSE-P-ALD-MONOMER.
BRENDAi4.1.2.4. 2026.
SABIO-RKP0A6L0.
UniPathwayiUPA00002; UER00468.

Names & Taxonomyi

Protein namesi
Recommended name:
Deoxyribose-phosphate aldolase (EC:4.1.2.4)
Short name:
DERA
Alternative name(s):
2-deoxy-D-ribose 5-phosphate aldolase
Phosphodeoxyriboaldolase
Short name:
Deoxyriboaldolase
Gene namesi
Name:deoC
Synonyms:dra, thyR
Ordered Locus Names:b4381, JW4344
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10221. deoC.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: UniProtKB
  • membrane Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 259259Deoxyribose-phosphate aldolasePRO_0000057296Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei167 – 1671N6-acetyllysine1 Publication

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiP0A6L0.
PRIDEiP0A6L0.

2D gel databases

SWISS-2DPAGEP0A6L0.

Interactioni

Subunit structurei

Monomer and homodimer.

Protein-protein interaction databases

IntActiP0A6L0. 8 interactions.
STRINGi511145.b4381.

Structurei

Secondary structure

1
259
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi3 – 1210Combined sources
Beta strandi15 – 184Combined sources
Helixi26 – 3510Combined sources
Beta strandi44 – 474Combined sources
Helixi50 – 523Combined sources
Helixi53 – 6210Combined sources
Beta strandi68 – 758Combined sources
Turni76 – 783Combined sources
Helixi83 – 9614Combined sources
Beta strandi99 – 1046Combined sources
Helixi107 – 1115Combined sources
Helixi116 – 13116Combined sources
Beta strandi135 – 1395Combined sources
Helixi142 – 1454Combined sources
Helixi148 – 16013Combined sources
Beta strandi164 – 1674Combined sources
Helixi179 – 19214Combined sources
Turni195 – 1973Combined sources
Beta strandi199 – 2013Combined sources
Beta strandi203 – 2053Combined sources
Helixi209 – 22315Combined sources
Turni230 – 2323Combined sources
Beta strandi235 – 2384Combined sources
Helixi240 – 2489Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JCJX-ray1.10A/B1-259[»]
1JCLX-ray1.05A/B1-259[»]
1KTNX-ray1.40A/B1-250[»]
1P1XX-ray0.99A/B1-259[»]
ProteinModelPortaliP0A6L0.
SMRiP0A6L0. Positions 1-250.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP0A6L0.

Family & Domainsi

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0274.
HOGENOMiHOG000241644.
InParanoidiP0A6L0.
KOiK01619.
OMAiPEVRIAT.
OrthoDBiEOG6QZMW5.
PhylomeDBiP0A6L0.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00592. DeoC_type2.
InterProiIPR013785. Aldolase_TIM.
IPR011343. DeoC.
IPR002915. DeoC/FbaB/lacD_aldolase.
IPR023649. DeoC_typeII.
[Graphical view]
PANTHERiPTHR10889. PTHR10889. 1 hit.
PfamiPF01791. DeoC. 1 hit.
[Graphical view]
PIRSFiPIRSF001357. DeoC. 1 hit.
TIGRFAMsiTIGR00126. deoC. 1 hit.

Sequencei

Sequence statusi: Complete.

P0A6L0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTDLKASSLR ALKLMDLTTL NDDDTDEKVI ALCHQAKTPV GNTAAICIYP
60 70 80 90 100
RFIPIARKTL KEQGTPEIRI ATVTNFPHGN DDIDIALAET RAAIAYGADE
110 120 130 140 150
VDVVFPYRAL MAGNEQVGFD LVKACKEACA AANVLLKVII ETGELKDEAL
160 170 180 190 200
IRKASEISIK AGADFIKTST GKVAVNATPE SARIMMEVIR DMGVEKTVGF
210 220 230 240 250
KPAGGVRTAE DAQKYLAIAD ELFGADWADA RHYRFGASSL LASLLKALGH

GDGKSASSY
Length:259
Mass (Da):27,734
Last modified:March 29, 2005 - v1
Checksum:iABA50C625195D494
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti18 – 181T → N in CAA26974 (PubMed:6749498).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03224 Genomic DNA. Translation: CAA26974.1.
U14003 Genomic DNA. Translation: AAA97277.1.
U00096 Genomic DNA. Translation: AAC77334.1.
AP009048 Genomic DNA. Translation: BAE78370.1.
PIRiA01102. ADECD.
RefSeqiNP_418798.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC77334; AAC77334; b4381.
BAE78370; BAE78370; BAE78370.
GeneIDi948902.
KEGGiecj:Y75_p4265.
eco:b4381.
PATRICi32124378. VBIEscCol129921_4529.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X03224 Genomic DNA. Translation: CAA26974.1.
U14003 Genomic DNA. Translation: AAA97277.1.
U00096 Genomic DNA. Translation: AAC77334.1.
AP009048 Genomic DNA. Translation: BAE78370.1.
PIRiA01102. ADECD.
RefSeqiNP_418798.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1JCJX-ray1.10A/B1-259[»]
1JCLX-ray1.05A/B1-259[»]
1KTNX-ray1.40A/B1-250[»]
1P1XX-ray0.99A/B1-259[»]
ProteinModelPortaliP0A6L0.
SMRiP0A6L0. Positions 1-250.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP0A6L0. 8 interactions.
STRINGi511145.b4381.

2D gel databases

SWISS-2DPAGEP0A6L0.

Proteomic databases

PaxDbiP0A6L0.
PRIDEiP0A6L0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77334; AAC77334; b4381.
BAE78370; BAE78370; BAE78370.
GeneIDi948902.
KEGGiecj:Y75_p4265.
eco:b4381.
PATRICi32124378. VBIEscCol129921_4529.

Organism-specific databases

EchoBASEiEB0217.
EcoGeneiEG10221. deoC.

Phylogenomic databases

eggNOGiCOG0274.
HOGENOMiHOG000241644.
InParanoidiP0A6L0.
KOiK01619.
OMAiPEVRIAT.
OrthoDBiEOG6QZMW5.
PhylomeDBiP0A6L0.

Enzyme and pathway databases

UniPathwayiUPA00002; UER00468.
BioCyciEcoCyc:DEOXYRIBOSE-P-ALD-MONOMER.
ECOL316407:JW4344-MONOMER.
MetaCyc:DEOXYRIBOSE-P-ALD-MONOMER.
BRENDAi4.1.2.4. 2026.
SABIO-RKP0A6L0.

Miscellaneous databases

EvolutionaryTraceiP0A6L0.
PROiP0A6L0.

Family and domain databases

Gene3Di3.20.20.70. 1 hit.
HAMAPiMF_00592. DeoC_type2.
InterProiIPR013785. Aldolase_TIM.
IPR011343. DeoC.
IPR002915. DeoC/FbaB/lacD_aldolase.
IPR023649. DeoC_typeII.
[Graphical view]
PANTHERiPTHR10889. PTHR10889. 1 hit.
PfamiPF01791. DeoC. 1 hit.
[Graphical view]
PIRSFiPIRSF001357. DeoC. 1 hit.
TIGRFAMsiTIGR00126. deoC. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The primary structure of Escherichia coli K12 2-deoxyribose 5-phosphate aldolase. Nucleotide sequence of the deoC gene and the amino acid sequence of the enzyme."
    Valentin-Hansen P., Boetius F., Hammer-Jespersen K., Svendsen I.
    Eur. J. Biochem. 125:561-566(1982) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  2. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
    Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
    Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "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].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli."
    Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F., Grishin N.V., Zhao Y.
    Mol. Cell. Proteomics 8:215-225(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-167, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: K12 / JW1106 and K12 / MG1655 / ATCC 47076.
  6. "Observation of covalent intermediates in an enzyme mechanism at atomic resolution."
    Heine A., DeSantis G., Luz J.G., Mitchell M., Wong C.-H., Wilson I.A.
    Science 294:369-374(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.05 ANGSTROMS), ACTIVE SITE, MUTAGENESIS.

Entry informationi

Entry nameiDEOC_ECOLI
AccessioniPrimary (citable) accession number: P0A6L0
Secondary accession number(s): P00882, Q2M5T6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: March 29, 2005
Last modified: June 24, 2015
This is version 94 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

External Data

Dasty 3

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 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.