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Deoxyribose-phosphate aldolase (DERA) (EC 4.1.2.4) (2-deoxy-D-ribose 5-phosphate aldolase) (Phosphodeoxyriboaldolase) (Deoxyriboaldolase)

 DEOC_ECOLI              Reviewed;         259 AA.
P0A6L0; P00882; Q2M5T6;
21-JUL-1986, integrated into UniProtKB/Swiss-Prot.
29-MAR-2005, sequence version 1.
28-MAR-2018, entry version 113.
RecName: Full=Deoxyribose-phosphate aldolase {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305};
Short=DERA {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000303|PubMed:7675789};
EC=4.1.2.4 {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000269|PubMed:11598300, ECO:0000269|PubMed:17905878, ECO:0000269|PubMed:6749498};
AltName: Full=2-deoxy-D-ribose 5-phosphate aldolase {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000303|PubMed:17905878, ECO:0000305};
AltName: Full=Phosphodeoxyriboaldolase {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305};
Short=Deoxyriboaldolase {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305};
Name=deoC {ECO:0000255|HAMAP-Rule:MF_00592,
ECO:0000303|PubMed:6749498}; Synonyms=dra, thyR;
OrderedLocusNames=b4381, JW4344;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-11, FUNCTION,
CATALYTIC ACTIVITY, AND SUBUNIT.
STRAIN=K12;
PubMed=6749498; DOI=10.1111/j.1432-1033.1982.tb06719.x;
Valentin-Hansen P., Boetius F., Hammer-Jespersen K., Svendsen I.;
"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.";
Eur. J. Biochem. 125:561-566(1982).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=7610040; DOI=10.1093/nar/23.12.2105;
Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.,
Blattner F.R.;
"Analysis of the Escherichia coli genome VI: DNA sequence of the
region from 92.8 through 100 minutes.";
Nucleic Acids Res. 23:2105-2119(1995).
[3]
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).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
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).
[5]
ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-167, AND IDENTIFICATION BY
MASS SPECTROMETRY.
STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
PubMed=18723842; DOI=10.1074/mcp.M800187-MCP200;
Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
Grishin N.V., Zhao Y.;
"Lysine acetylation is a highly abundant and evolutionarily conserved
modification in Escherichia coli.";
Mol. Cell. Proteomics 8:215-225(2009).
[6]
CRYSTALLIZATION, AND SUBUNIT.
PubMed=7675789; DOI=10.1002/prot.340220110;
Stura E.A., Ghosh S., Garcia-Junceda E., Chen L., Wong C.H.,
Wilson I.A.;
"Crystallization and preliminary crystallographic data for class I
deoxyribose-5-phosphate aldolase from Escherichia coli: an application
of reverse screening.";
Proteins 22:67-72(1995).
[7]
FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=17905878; DOI=10.1128/AEM.01101-07;
Sakuraba H., Yoneda K., Yoshihara K., Satoh K., Kawakami R., Uto Y.,
Tsuge H., Takahashi K., Hori H., Ohshima T.;
"Sequential aldol condensation catalyzed by hyperthermophilic 2-deoxy-
d-ribose-5-phosphate aldolase.";
Appl. Environ. Microbiol. 73:7427-7434(2007).
[8] {ECO:0000244|PDB:1JCJ, ECO:0000244|PDB:1JCL}
X-RAY CRYSTALLOGRAPHY (1.05 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
ACTIVE SITE, AND MUTAGENESIS OF CYS-47; ASP-102; LYS-137; LYS-167;
LYS-201 AND TYR-259.
PubMed=11598300; DOI=10.1126/science.1063601;
Heine A., DeSantis G., Luz J.G., Mitchell M., Wong C.-H., Wilson I.A.;
"Observation of covalent intermediates in an enzyme mechanism at
atomic resolution.";
Science 294:369-374(2001).
[9] {ECO:0000244|PDB:1KTN}
X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF 1-250.
Zhang R., Joachimiak A., Edwards A., Skarina T., Evdokimova E.,
Savchenko A.;
"The 1.5A crystal structure of 2-deoxyribose-5-phosphate aldolase.";
Submitted (JAN-2002) to the PDB data bank.
[10] {ECO:0000244|PDB:1P1X}
X-RAY CRYSTALLOGRAPHY (0.99 ANGSTROMS), AND ACTIVE SITE.
PubMed=15476818; DOI=10.1016/j.jmb.2004.08.066;
Heine A., Luz J.G., Wong C.H., Wilson I.A.;
"Analysis of the class I aldolase binding site architecture based on
the crystal structure of 2-deoxyribose-5-phosphate aldolase at 0.99A
resolution.";
J. Mol. Biol. 343:1019-1034(2004).
[11] {ECO:0000244|PDB:5EKY, ECO:0000244|PDB:5EL1, ECO:0000244|PDB:5EMU}
X-RAY CRYSTALLOGRAPHY (1.10 ANGSTROMS) OF MUTANT GLU-58/TRP-96.
DOI=10.1039/c5sc04574f;
Dick M., Hartmann R., Weiergraeber O.H., Bisterfeld C., Classen T.,
Schwarten M., Neudecker P., Willbold D., Pietruszka J.;
"Mechanism-based inhibition of an aldolase at high concentrations of
its natural substrate acetaldehyde: structural insights and protective
strategies.";
Chem. Sci. 7:4492-4502(2016).
-!- FUNCTION: Catalyzes a reversible aldol reaction between
acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-
D-ribose 5-phosphate. {ECO:0000255|HAMAP-Rule:MF_00592,
ECO:0000269|PubMed:11598300, ECO:0000269|PubMed:17905878,
ECO:0000269|PubMed:6749498}.
-!- CATALYTIC ACTIVITY: 2-deoxy-D-ribose 5-phosphate = D-
glyceraldehyde 3-phosphate + acetaldehyde. {ECO:0000255|HAMAP-
Rule:MF_00592, ECO:0000269|PubMed:11598300,
ECO:0000269|PubMed:17905878, ECO:0000269|PubMed:6749498}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.23 mM for 2-deoxy-D-ribose 5-phosphate
{ECO:0000269|PubMed:17905878};
pH dependence:
Optimum pH is 7.5 for 2-deoxy-D-ribose 5-phosphate cleavage.
{ECO:0000269|PubMed:17905878};
-!- PATHWAY: Carbohydrate degradation; 2-deoxy-D-ribose 1-phosphate
degradation; D-glyceraldehyde 3-phosphate and acetaldehyde from 2-
deoxy-alpha-D-ribose 1-phosphate: step 2/2. {ECO:0000255|HAMAP-
Rule:MF_00592, ECO:0000305}.
-!- SUBUNIT: Monomer and homodimer. {ECO:0000269|PubMed:6749498,
ECO:0000269|PubMed:7675789}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00592,
ECO:0000305}.
-!- SIMILARITY: Belongs to the DeoC/FbaB aldolase family. DeoC type 2
subfamily. {ECO:0000255|HAMAP-Rule:MF_00592, ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; X03224; CAA26974.1; -; Genomic_DNA.
EMBL; U14003; AAA97277.1; -; Genomic_DNA.
EMBL; U00096; AAC77334.1; -; Genomic_DNA.
EMBL; AP009048; BAE78370.1; -; Genomic_DNA.
PIR; A01102; ADECD.
RefSeq; NP_418798.1; NC_000913.3.
RefSeq; WP_001298497.1; NZ_LN832404.1.
PDB; 1JCJ; X-ray; 1.10 A; A/B=1-259.
PDB; 1JCL; X-ray; 1.05 A; A/B=1-259.
PDB; 1KTN; X-ray; 1.40 A; A/B=1-250.
PDB; 1P1X; X-ray; 0.99 A; A/B=1-259.
PDB; 5EKY; X-ray; 1.10 A; A=1-259.
PDB; 5EL1; X-ray; 1.25 A; A=1-259.
PDB; 5EMU; X-ray; 1.50 A; A=1-259.
PDBsum; 1JCJ; -.
PDBsum; 1JCL; -.
PDBsum; 1KTN; -.
PDBsum; 1P1X; -.
PDBsum; 5EKY; -.
PDBsum; 5EL1; -.
PDBsum; 5EMU; -.
ProteinModelPortal; P0A6L0; -.
SMR; P0A6L0; -.
BioGrid; 4263350; 25.
IntAct; P0A6L0; 8.
STRING; 316385.ECDH10B_4539; -.
DrugBank; DB04087; Open Form of 2'-Deoxy-Ribofuranose-5'-Phosphate.
iPTMnet; P0A6L0; -.
SWISS-2DPAGE; P0A6L0; -.
EPD; P0A6L0; -.
PaxDb; P0A6L0; -.
PRIDE; P0A6L0; -.
EnsemblBacteria; AAC77334; AAC77334; b4381.
EnsemblBacteria; BAE78370; BAE78370; BAE78370.
GeneID; 948902; -.
KEGG; ecj:JW4344; -.
KEGG; eco:b4381; -.
PATRIC; fig|1411691.4.peg.2304; -.
EchoBASE; EB0217; -.
EcoGene; EG10221; deoC.
eggNOG; ENOG4105FCI; Bacteria.
eggNOG; COG0274; LUCA.
HOGENOM; HOG000241644; -.
InParanoid; P0A6L0; -.
KO; K01619; -.
OMA; MNACIPP; -.
PhylomeDB; P0A6L0; -.
BioCyc; EcoCyc:DEOXYRIBOSE-P-ALD-MONOMER; -.
BioCyc; MetaCyc:DEOXYRIBOSE-P-ALD-MONOMER; -.
BRENDA; 4.1.2.4; 2026.
SABIO-RK; P0A6L0; -.
UniPathway; UPA00002; UER00468.
EvolutionaryTrace; P0A6L0; -.
PRO; PR:P0A6L0; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005829; C:cytosol; IDA:EcoCyc.
GO; GO:0016020; C:membrane; HDA:UniProtKB.
GO; GO:0004139; F:deoxyribose-phosphate aldolase activity; IDA:EcoCyc.
GO; GO:0016829; F:lyase activity; IDA:EcoliWiki.
GO; GO:0016052; P:carbohydrate catabolic process; IDA:EcoliWiki.
GO; GO:0006974; P:cellular response to DNA damage stimulus; IEP:EcoliWiki.
GO; GO:0009264; P:deoxyribonucleotide catabolic process; IMP:EcoliWiki.
GO; GO:0046386; P:deoxyribose phosphate catabolic process; IEA:UniProtKB-UniPathway.
GO; GO:0015949; P:nucleobase-containing small molecule interconversion; IMP:EcoliWiki.
CDD; cd00959; DeoC; 1.
Gene3D; 3.20.20.70; -; 1.
HAMAP; MF_00592; DeoC_type2; 1.
InterPro; IPR013785; Aldolase_TIM.
InterPro; IPR011343; DeoC.
InterPro; IPR002915; DeoC/FbaB/lacD_aldolase.
InterPro; IPR023649; DeoC_typeII.
PANTHER; PTHR10889; PTHR10889; 1.
Pfam; PF01791; DeoC; 1.
PIRSF; PIRSF001357; DeoC; 1.
SMART; SM01133; DeoC; 1.
TIGRFAMs; TIGR00126; deoC; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Complete proteome; Cytoplasm;
Direct protein sequencing; Lyase; Reference proteome; Schiff base.
CHAIN 1 259 Deoxyribose-phosphate aldolase.
/FTId=PRO_0000057296.
ACT_SITE 102 102 Proton donor/acceptor.
{ECO:0000255|HAMAP-Rule:MF_00592,
ECO:0000305|PubMed:11598300}.
ACT_SITE 167 167 Schiff-base intermediate with
acetaldehyde. {ECO:0000255|HAMAP-
Rule:MF_00592,
ECO:0000269|PubMed:11598300,
ECO:0000305|PubMed:15476818}.
ACT_SITE 201 201 Proton donor/acceptor.
{ECO:0000255|HAMAP-Rule:MF_00592,
ECO:0000305|PubMed:11598300,
ECO:0000305|PubMed:15476818}.
MOD_RES 167 167 N6-acetyllysine.
{ECO:0000269|PubMed:18723842}.
MUTAGEN 47 47 C->A,S: 3-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 102 102 D->E: 44-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 102 102 D->L: 2000-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 102 102 D->N: 1500-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 137 137 K->L: 20-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 167 167 K->L: 1000-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 167 167 K->R: 20-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 201 201 K->L: 1500-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 201 201 K->R: 1000-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
MUTAGEN 259 259 Y->F: 200-fold decrease in catalytic
efficiency.
{ECO:0000269|PubMed:11598300}.
CONFLICT 18 18 T -> N (in Ref. 1; CAA26974).
{ECO:0000305}.
HELIX 3 12 {ECO:0000244|PDB:1P1X}.
STRAND 15 18 {ECO:0000244|PDB:1P1X}.
HELIX 26 35 {ECO:0000244|PDB:1P1X}.
STRAND 44 47 {ECO:0000244|PDB:1P1X}.
HELIX 50 52 {ECO:0000244|PDB:1P1X}.
HELIX 53 62 {ECO:0000244|PDB:1P1X}.
STRAND 68 75 {ECO:0000244|PDB:1P1X}.
TURN 76 78 {ECO:0000244|PDB:1P1X}.
HELIX 83 96 {ECO:0000244|PDB:1P1X}.
STRAND 99 104 {ECO:0000244|PDB:1P1X}.
HELIX 107 111 {ECO:0000244|PDB:1P1X}.
HELIX 116 131 {ECO:0000244|PDB:1P1X}.
STRAND 135 139 {ECO:0000244|PDB:1P1X}.
HELIX 142 145 {ECO:0000244|PDB:1P1X}.
HELIX 148 160 {ECO:0000244|PDB:1P1X}.
STRAND 164 167 {ECO:0000244|PDB:1P1X}.
STRAND 171 174 {ECO:0000244|PDB:5EKY}.
HELIX 179 192 {ECO:0000244|PDB:1P1X}.
TURN 195 197 {ECO:0000244|PDB:1P1X}.
STRAND 199 201 {ECO:0000244|PDB:1P1X}.
STRAND 203 205 {ECO:0000244|PDB:1P1X}.
HELIX 209 223 {ECO:0000244|PDB:1P1X}.
TURN 230 232 {ECO:0000244|PDB:1P1X}.
STRAND 235 238 {ECO:0000244|PDB:1P1X}.
HELIX 240 248 {ECO:0000244|PDB:1P1X}.
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


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