DEOC_ECOLI
ID DEOC_ECOLI Reviewed; 259 AA.
AC P0A6L0; P00882; Q2M5T6;
DT 21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
DT 29-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 133.
DE RecName: Full=Deoxyribose-phosphate aldolase {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305};
DE Short=DERA {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000303|PubMed:7675789, ECO:0000303|Ref.5};
DE EC=4.1.2.4 {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000269|PubMed:11598300, ECO:0000269|PubMed:17905878, ECO:0000269|PubMed:6749498};
DE AltName: Full=2-deoxy-D-ribose 5-phosphate aldolase {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000303|PubMed:17905878, ECO:0000305};
DE AltName: Full=Phosphodeoxyriboaldolase {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305};
DE Short=Deoxyriboaldolase {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305};
GN Name=deoC {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000303|PubMed:6749498};
GN Synonyms=dra, thyR; OrderedLocusNames=b4381, JW4344;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-11, FUNCTION,
RP CATALYTIC ACTIVITY, AND SUBUNIT.
RC STRAIN=K12;
RX PubMed=6749498; DOI=10.1111/j.1432-1033.1982.tb06719.x;
RA Valentin-Hansen P., Boetius F., Hammer-Jespersen K., Svendsen I.;
RT "The primary structure of Escherichia coli K12 2-deoxyribose 5-phosphate
RT aldolase. Nucleotide sequence of the deoC gene and the amino acid sequence
RT of the enzyme.";
RL Eur. J. Biochem. 125:561-566(1982).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7610040; DOI=10.1093/nar/23.12.2105;
RA Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome VI: DNA sequence of the region
RT from 92.8 through 100 minutes.";
RL Nucleic Acids Res. 23:2105-2119(1995).
RN [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
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 [5]
RP FUNCTION.
RX DOI=10.1021/ja00097a082;
RA Gijsen H.J.M., Wong C.H.;
RT "Unprecedented asymmetric aldol reactions with three aldehyde substrates
RT catalyzed by 2-deoxyribose-5-phosphate aldolase.";
RL J. Am. Chem. Soc. 116:8422-8423(1994).
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-167, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX PubMed=18723842; DOI=10.1074/mcp.m800187-mcp200;
RA Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA Grishin N.V., Zhao Y.;
RT "Lysine acetylation is a highly abundant and evolutionarily conserved
RT modification in Escherichia coli.";
RL Mol. Cell. Proteomics 8:215-225(2009).
RN [7]
RP CRYSTALLIZATION, AND SUBUNIT.
RX PubMed=7675789; DOI=10.1002/prot.340220110;
RA Stura E.A., Ghosh S., Garcia-Junceda E., Chen L., Wong C.H., Wilson I.A.;
RT "Crystallization and preliminary crystallographic data for class I
RT deoxyribose-5-phosphate aldolase from Escherichia coli: an application of
RT reverse screening.";
RL Proteins 22:67-72(1995).
RN [8]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17905878; DOI=10.1128/aem.01101-07;
RA Sakuraba H., Yoneda K., Yoshihara K., Satoh K., Kawakami R., Uto Y.,
RA Tsuge H., Takahashi K., Hori H., Ohshima T.;
RT "Sequential aldol condensation catalyzed by hyperthermophilic 2-deoxy-d-
RT ribose-5-phosphate aldolase.";
RL Appl. Environ. Microbiol. 73:7427-7434(2007).
RN [9] {ECO:0007744|PDB:1JCJ, ECO:0007744|PDB:1JCL}
RP X-RAY CRYSTALLOGRAPHY (1.05 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
RP ACTIVE SITE, AND MUTAGENESIS OF CYS-47; ASP-102; LYS-137; LYS-167; LYS-201
RP AND TYR-259.
RX PubMed=11598300; DOI=10.1126/science.1063601;
RA Heine A., DeSantis G., Luz J.G., Mitchell M., Wong C.-H., Wilson I.A.;
RT "Observation of covalent intermediates in an enzyme mechanism at atomic
RT resolution.";
RL Science 294:369-374(2001).
RN [10] {ECO:0007744|PDB:1KTN}
RP X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF 1-250.
RA Zhang R., Joachimiak A., Edwards A., Skarina T., Evdokimova E.,
RA Savchenko A.;
RT "The 1.5A crystal structure of 2-deoxyribose-5-phosphate aldolase.";
RL Submitted (JAN-2002) to the PDB data bank.
RN [11] {ECO:0007744|PDB:1P1X}
RP X-RAY CRYSTALLOGRAPHY (0.99 ANGSTROMS), AND ACTIVE SITE.
RX PubMed=15476818; DOI=10.1016/j.jmb.2004.08.066;
RA Heine A., Luz J.G., Wong C.H., Wilson I.A.;
RT "Analysis of the class I aldolase binding site architecture based on the
RT crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A
RT resolution.";
RL J. Mol. Biol. 343:1019-1034(2004).
RN [12] {ECO:0007744|PDB:5EKY, ECO:0007744|PDB:5EL1, ECO:0007744|PDB:5EMU}
RP X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) OF MUTANT GLU-58/TRP-96.
RX DOI=10.1039/c5sc04574f;
RA Dick M., Hartmann R., Weiergraeber O.H., Bisterfeld C., Classen T.,
RA Schwarten M., Neudecker P., Willbold D., Pietruszka J.;
RT "Mechanism-based inhibition of an aldolase at high concentrations of its
RT natural substrate acetaldehyde: structural insights and protective
RT strategies.";
RL Chem. Sci. 7:4492-4502(2016).
CC -!- FUNCTION: Catalyzes a reversible aldol reaction between acetaldehyde
CC and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-
CC phosphate (PubMed:11598300, PubMed:17905878, PubMed:6749498). Can also
CC catalyze the double aldol condensation of three acetaldehyde molecules,
CC leading to the formation of 2,4,6-trideoxyhexose (Ref.5).
CC {ECO:0000269|PubMed:11598300, ECO:0000269|PubMed:17905878,
CC ECO:0000269|PubMed:6749498, ECO:0000269|Ref.5}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-deoxy-D-ribose 5-phosphate = acetaldehyde + D-glyceraldehyde
CC 3-phosphate; Xref=Rhea:RHEA:12821, ChEBI:CHEBI:15343,
CC ChEBI:CHEBI:59776, ChEBI:CHEBI:62877; EC=4.1.2.4;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00592,
CC ECO:0000269|PubMed:11598300, ECO:0000269|PubMed:17905878,
CC ECO:0000269|PubMed:6749498};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.23 mM for 2-deoxy-D-ribose 5-phosphate
CC {ECO:0000269|PubMed:17905878};
CC pH dependence:
CC Optimum pH is 7.5 for 2-deoxy-D-ribose 5-phosphate cleavage.
CC {ECO:0000269|PubMed:17905878};
CC -!- PATHWAY: Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate
CC degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-
CC deoxy-alpha-D-ribose 1-phosphate: step 2/2. {ECO:0000255|HAMAP-
CC Rule:MF_00592, ECO:0000305}.
CC -!- SUBUNIT: Monomer and homodimer. {ECO:0000269|PubMed:6749498,
CC ECO:0000269|PubMed:7675789}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00592,
CC ECO:0000305}.
CC -!- SIMILARITY: Belongs to the DeoC/FbaB aldolase family. DeoC type 2
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305}.
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DR EMBL; X03224; CAA26974.1; -; Genomic_DNA.
DR EMBL; U14003; AAA97277.1; -; Genomic_DNA.
DR EMBL; U00096; AAC77334.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE78370.1; -; Genomic_DNA.
DR PIR; A01102; ADECD.
DR RefSeq; NP_418798.1; NC_000913.3.
DR RefSeq; WP_001298497.1; NZ_LN832404.1.
DR PDB; 1JCJ; X-ray; 1.10 A; A/B=1-259.
DR PDB; 1JCL; X-ray; 1.05 A; A/B=1-259.
DR PDB; 1KTN; X-ray; 1.40 A; A/B=1-250.
DR PDB; 1P1X; X-ray; 0.99 A; A/B=1-259.
DR PDB; 5EKY; X-ray; 1.10 A; A=1-259.
DR PDB; 5EL1; X-ray; 1.25 A; A=1-259.
DR PDB; 5EMU; X-ray; 1.50 A; A=1-259.
DR PDB; 6Z9H; X-ray; 1.72 A; A/B=2-259.
DR PDB; 6Z9I; X-ray; 1.86 A; A/B=1-250.
DR PDB; 6Z9J; X-ray; 1.50 A; A/B=1-250.
DR PDBsum; 1JCJ; -.
DR PDBsum; 1JCL; -.
DR PDBsum; 1KTN; -.
DR PDBsum; 1P1X; -.
DR PDBsum; 5EKY; -.
DR PDBsum; 5EL1; -.
DR PDBsum; 5EMU; -.
DR PDBsum; 6Z9H; -.
DR PDBsum; 6Z9I; -.
DR PDBsum; 6Z9J; -.
DR AlphaFoldDB; P0A6L0; -.
DR SMR; P0A6L0; -.
DR BioGRID; 4263350; 25.
DR IntAct; P0A6L0; 8.
DR STRING; 511145.b4381; -.
DR DrugBank; DB04087; Open Form of 2'-Deoxy-Ribofuranose-5'-Phosphate.
DR iPTMnet; P0A6L0; -.
DR SWISS-2DPAGE; P0A6L0; -.
DR jPOST; P0A6L0; -.
DR PaxDb; P0A6L0; -.
DR PRIDE; P0A6L0; -.
DR EnsemblBacteria; AAC77334; AAC77334; b4381.
DR EnsemblBacteria; BAE78370; BAE78370; BAE78370.
DR GeneID; 67416058; -.
DR GeneID; 948902; -.
DR KEGG; ecj:JW4344; -.
DR KEGG; eco:b4381; -.
DR PATRIC; fig|1411691.4.peg.2304; -.
DR EchoBASE; EB0217; -.
DR eggNOG; COG0274; Bacteria.
DR HOGENOM; CLU_053595_3_1_6; -.
DR InParanoid; P0A6L0; -.
DR OMA; MNACIPP; -.
DR PhylomeDB; P0A6L0; -.
DR BioCyc; EcoCyc:DEOXYRIBOSE-P-ALD-MON; -.
DR BioCyc; MetaCyc:DEOXYRIBOSE-P-ALD-MON; -.
DR BRENDA; 4.1.2.4; 2026.
DR SABIO-RK; P0A6L0; -.
DR UniPathway; UPA00002; UER00468.
DR EvolutionaryTrace; P0A6L0; -.
DR PRO; PR:P0A6L0; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0016020; C:membrane; HDA:UniProtKB.
DR GO; GO:0004139; F:deoxyribose-phosphate aldolase activity; IDA:EcoCyc.
DR GO; GO:0016829; F:lyase activity; IDA:EcoliWiki.
DR GO; GO:0016052; P:carbohydrate catabolic process; IDA:EcoliWiki.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
DR GO; GO:0009264; P:deoxyribonucleotide catabolic process; IMP:EcoliWiki.
DR GO; GO:0046386; P:deoxyribose phosphate catabolic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IMP:EcoliWiki.
DR CDD; cd00959; DeoC; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_00592; DeoC_type2; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR011343; DeoC.
DR InterPro; IPR002915; DeoC/FbaB/LacD_aldolase.
DR InterPro; IPR023649; DeoC_typeII.
DR PANTHER; PTHR10889; PTHR10889; 1.
DR Pfam; PF01791; DeoC; 1.
DR PIRSF; PIRSF001357; DeoC; 1.
DR SMART; SM01133; DeoC; 1.
DR TIGRFAMs; TIGR00126; deoC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Direct protein sequencing; Lyase;
KW Reference proteome; Schiff base.
FT CHAIN 1..259
FT /note="Deoxyribose-phosphate aldolase"
FT /id="PRO_0000057296"
FT ACT_SITE 102
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00592,
FT ECO:0000305|PubMed:11598300"
FT ACT_SITE 167
FT /note="Schiff-base intermediate with acetaldehyde"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00592,
FT ECO:0000269|PubMed:11598300, ECO:0000305|PubMed:15476818"
FT ACT_SITE 201
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00592,
FT ECO:0000305|PubMed:11598300, ECO:0000305|PubMed:15476818"
FT MOD_RES 167
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT MUTAGEN 47
FT /note="C->A,S: 3-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 102
FT /note="D->E: 44-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 102
FT /note="D->L: 2000-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 102
FT /note="D->N: 1500-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 137
FT /note="K->L: 20-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 167
FT /note="K->L: 1000-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 167
FT /note="K->R: 20-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 201
FT /note="K->L: 1500-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 201
FT /note="K->R: 1000-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT MUTAGEN 259
FT /note="Y->F: 200-fold decrease in catalytic efficiency."
FT /evidence="ECO:0000269|PubMed:11598300"
FT CONFLICT 18
FT /note="T -> N (in Ref. 1; CAA26974)"
FT /evidence="ECO:0000305"
FT HELIX 3..12
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 15..18
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 26..35
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 44..47
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 53..62
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 68..75
FT /evidence="ECO:0007829|PDB:1P1X"
FT TURN 76..78
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 83..96
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 99..104
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 107..111
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 116..131
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 135..139
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 142..145
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 148..160
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 164..167
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:5EKY"
FT HELIX 179..192
FT /evidence="ECO:0007829|PDB:1P1X"
FT TURN 195..197
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 199..201
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 209..223
FT /evidence="ECO:0007829|PDB:1P1X"
FT TURN 230..232
FT /evidence="ECO:0007829|PDB:1P1X"
FT STRAND 235..238
FT /evidence="ECO:0007829|PDB:1P1X"
FT HELIX 240..248
FT /evidence="ECO:0007829|PDB:1P1X"
SQ SEQUENCE 259 AA; 27734 MW; ABA50C625195D494 CRC64;
MTDLKASSLR ALKLMDLTTL NDDDTDEKVI ALCHQAKTPV GNTAAICIYP RFIPIARKTL
KEQGTPEIRI ATVTNFPHGN DDIDIALAET RAAIAYGADE VDVVFPYRAL MAGNEQVGFD
LVKACKEACA AANVLLKVII ETGELKDEAL IRKASEISIK AGADFIKTST GKVAVNATPE
SARIMMEVIR DMGVEKTVGF KPAGGVRTAE DAQKYLAIAD ELFGADWADA RHYRFGASSL
LASLLKALGH GDGKSASSY
