RHAD_ECOLI
ID RHAD_ECOLI Reviewed; 274 AA.
AC P32169; Q2M8J9;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1993, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Rhamnulose-1-phosphate aldolase;
DE EC=4.1.2.19 {ECO:0000269|PubMed:12962479};
GN Name=rhaD; Synonyms=rhuA; OrderedLocusNames=b3902, JW3873;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=8396120; DOI=10.1128/jb.175.17.5585-5594.1993;
RA Moralejo P., Egan S.M., Hidalgo E.F., Aguilar J.;
RT "Sequencing and characterization of a gene cluster encoding the enzymes for
RT L-rhamnose metabolism in Escherichia coli.";
RL J. Bacteriol. 175:5585-5594(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8346018; DOI=10.1093/nar/21.15.3391;
RA Plunkett G. III, Burland V., Daniels D.L., Blattner F.R.;
RT "Analysis of the Escherichia coli genome. III. DNA sequence of the region
RT from 87.2 to 89.2 minutes.";
RL Nucleic Acids Res. 21:3391-3398(1993).
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 INDUCTION.
RC STRAIN=ECL116;
RX PubMed=8230210; DOI=10.1006/jmbi.1993.1565;
RA Egan S.M., Schleif R.F.;
RT "A regulatory cascade in the induction of rhaBAD.";
RL J. Mol. Biol. 234:87-98(1993).
RN [6]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [7]
RP INDUCTION.
RX PubMed=10852886; DOI=10.1128/jb.182.12.3529-3535.2000;
RA Holcroft C.C., Egan S.M.;
RT "Roles of cyclic AMP receptor protein and the carboxyl-terminal domain of
RT the alpha subunit in transcription activation of the Escherichia coli
RT rhaBAD operon.";
RL J. Bacteriol. 182:3529-3535(2000).
RN [8]
RP FUNCTION.
RX PubMed=25848029; DOI=10.1073/pnas.1423570112;
RA Huang H., Pandya C., Liu C., Al-Obaidi N.F., Wang M., Zheng L.,
RA Toews Keating S., Aono M., Love J.D., Evans B., Seidel R.D.,
RA Hillerich B.S., Garforth S.J., Almo S.C., Mariano P.S., Dunaway-Mariano D.,
RA Allen K.N., Farelli J.D.;
RT "Panoramic view of a superfamily of phosphatases through substrate
RT profiling.";
RL Proc. Natl. Acad. Sci. U.S.A. 112:E1974-E1983(2015).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH ZINC, COFACTOR,
RP SUBUNIT, AND ACTIVE SITE.
RX PubMed=11976494; DOI=10.1107/s0907444902004614;
RA Kroemer M., Schulz G.E.;
RT "The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by
RT low-resolution SIR phasing and 20-fold NCS averaging.";
RL Acta Crystallogr. D 58:824-832(2002).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) IN COMPLEX WITH ZINC, FUNCTION,
RP CATALYTIC ACTIVITY, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVE SITE,
RP AND MUTAGENESIS OF ARG-28; ASN-29; GLU-117; GLU-171 AND GLU-192.
RX PubMed=12962479; DOI=10.1021/bi0349266;
RA Kroemer M., Merkel I., Schulz G.E.;
RT "Structure and catalytic mechanism of L-rhamnulose-1-phosphate aldolase.";
RL Biochemistry 42:10560-10568(2003).
CC -!- FUNCTION: Catalyzes the reversible cleavage of L-rhamnulose-1-phosphate
CC to dihydroxyacetone phosphate (DHAP) and L-lactaldehyde
CC (PubMed:12962479). Also catalyzes the dephosphorylation of phospho-
CC serine in vitro (PubMed:25848029). {ECO:0000269|PubMed:12962479,
CC ECO:0000269|PubMed:25848029}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-rhamnulose 1-phosphate = (S)-lactaldehyde + dihydroxyacetone
CC phosphate; Xref=Rhea:RHEA:19689, ChEBI:CHEBI:18041,
CC ChEBI:CHEBI:57642, ChEBI:CHEBI:58313; EC=4.1.2.19;
CC Evidence={ECO:0000269|PubMed:12962479};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:11976494, ECO:0000269|PubMed:12962479};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:11976494,
CC ECO:0000269|PubMed:12962479};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.48 mM for L-rhamnulose 1-phosphate (at 37 degrees Celsius)
CC {ECO:0000269|PubMed:12962479};
CC -!- PATHWAY: Carbohydrate degradation; L-rhamnose degradation; glycerone
CC phosphate from L-rhamnose: step 3/3.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:11976494}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- INDUCTION: Induced by L-rhamnose via the RhaR-RhaS regulatory cascade.
CC Binding of the cAMP receptor protein (CRP) is required for full
CC expression. {ECO:0000269|PubMed:10852886, ECO:0000269|PubMed:8230210}.
CC -!- SIMILARITY: Belongs to the aldolase class II family. RhaD subfamily.
CC {ECO:0000305}.
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DR EMBL; X60472; CAA43003.1; -; Genomic_DNA.
DR EMBL; L19201; AAB03035.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76884.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77407.1; -; Genomic_DNA.
DR PIR; C48649; C48649.
DR RefSeq; NP_418338.1; NC_000913.3.
DR RefSeq; WP_001179745.1; NZ_LN832404.1.
DR PDB; 1GT7; X-ray; 2.70 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P/Q/R/S/T=1-274.
DR PDB; 1OJR; X-ray; 1.35 A; A=1-274.
DR PDB; 2UYU; X-ray; 1.96 A; A/E=1-274.
DR PDB; 2UYV; X-ray; 2.20 A; A/B/C/D=1-274.
DR PDB; 2V29; X-ray; 2.03 A; A/B=1-274.
DR PDB; 2V2A; X-ray; 1.75 A; A=1-274.
DR PDB; 2V2B; X-ray; 1.50 A; A=1-274.
DR PDB; 2V9E; X-ray; 1.58 A; A/B=1-272.
DR PDB; 2V9F; X-ray; 2.10 A; A=1-272.
DR PDB; 2V9G; X-ray; 2.70 A; A/B/C/D=1-274.
DR PDB; 2V9I; X-ray; 1.80 A; A/B=1-273.
DR PDB; 2V9L; X-ray; 1.23 A; A=1-274.
DR PDB; 2V9M; X-ray; 1.30 A; A/B=1-274.
DR PDB; 2V9N; X-ray; 1.40 A; A/B/C/D=1-274.
DR PDB; 2V9O; X-ray; 1.95 A; A/E=1-274.
DR PDBsum; 1GT7; -.
DR PDBsum; 1OJR; -.
DR PDBsum; 2UYU; -.
DR PDBsum; 2UYV; -.
DR PDBsum; 2V29; -.
DR PDBsum; 2V2A; -.
DR PDBsum; 2V2B; -.
DR PDBsum; 2V9E; -.
DR PDBsum; 2V9F; -.
DR PDBsum; 2V9G; -.
DR PDBsum; 2V9I; -.
DR PDBsum; 2V9L; -.
DR PDBsum; 2V9M; -.
DR PDBsum; 2V9N; -.
DR PDBsum; 2V9O; -.
DR AlphaFoldDB; P32169; -.
DR SMR; P32169; -.
DR IntAct; P32169; 7.
DR STRING; 511145.b3902; -.
DR DrugBank; DB03026; Phosphoglycolohydroxamic Acid.
DR PaxDb; P32169; -.
DR PRIDE; P32169; -.
DR EnsemblBacteria; AAC76884; AAC76884; b3902.
DR EnsemblBacteria; BAE77407; BAE77407; BAE77407.
DR GeneID; 948401; -.
DR KEGG; ecj:JW3873; -.
DR KEGG; eco:b3902; -.
DR PATRIC; fig|1411691.4.peg.2804; -.
DR EchoBASE; EB1812; -.
DR eggNOG; COG0235; Bacteria.
DR HOGENOM; CLU_076831_0_0_6; -.
DR InParanoid; P32169; -.
DR OMA; SHFMSHI; -.
DR PhylomeDB; P32169; -.
DR BioCyc; EcoCyc:RHAMNULPALDOL-MON; -.
DR BioCyc; MetaCyc:RHAMNULPALDOL-MON; -.
DR BRENDA; 4.1.2.19; 2026.
DR SABIO-RK; P32169; -.
DR UniPathway; UPA00541; UER00603.
DR EvolutionaryTrace; P32169; -.
DR PRO; PR:P32169; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0016832; F:aldehyde-lyase activity; IBA:GO_Central.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008994; F:rhamnulose-1-phosphate aldolase activity; IDA:EcoCyc.
DR GO; GO:0019323; P:pentose catabolic process; IBA:GO_Central.
DR GO; GO:0019301; P:rhamnose catabolic process; IMP:EcoCyc.
DR Gene3D; 3.40.225.10; -; 1.
DR HAMAP; MF_00770; RhaD; 1.
DR InterPro; IPR001303; Aldolase_II/adducin_N.
DR InterPro; IPR036409; Aldolase_II/adducin_N_sf.
DR InterPro; IPR013447; Rhamnulose-1-P_Aldolase.
DR Pfam; PF00596; Aldolase_II; 1.
DR SMART; SM01007; Aldolase_II; 1.
DR SUPFAM; SSF53639; SSF53639; 1.
DR TIGRFAMs; TIGR02624; rhamnu_1P_ald; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Lyase; Metal-binding; Reference proteome;
KW Rhamnose metabolism; Zinc.
FT CHAIN 1..274
FT /note="Rhamnulose-1-phosphate aldolase"
FT /id="PRO_0000209657"
FT ACT_SITE 117
FT /evidence="ECO:0000269|PubMed:11976494,
FT ECO:0000269|PubMed:12962479"
FT BINDING 141
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:11976494,
FT ECO:0000269|PubMed:12962479"
FT BINDING 143
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:11976494,
FT ECO:0000269|PubMed:12962479"
FT BINDING 212
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000269|PubMed:11976494,
FT ECO:0000269|PubMed:12962479"
FT MUTAGEN 28
FT /note="R->A,S: Severe loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:12962479"
FT MUTAGEN 29
FT /note="N->A: Severe loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:12962479"
FT MUTAGEN 117
FT /note="E->Q: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:12962479"
FT MUTAGEN 171
FT /note="E->S,A,Q: Loss of enzymatic activity."
FT /evidence="ECO:0000269|PubMed:12962479"
FT MUTAGEN 192
FT /note="E->A: No effect on enzymatic activity."
FT /evidence="ECO:0000269|PubMed:12962479"
FT HELIX 4..6
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 8..22
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 31..36
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 39..42
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 43..48
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 54..57
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 69..74
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:2V9L"
FT TURN 82..84
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 86..89
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 90..95
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 99..107
FT /evidence="ECO:0007829|PDB:2V9L"
FT TURN 109..111
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 113..115
FT /evidence="ECO:0007829|PDB:2V9M"
FT HELIX 118..131
FT /evidence="ECO:0007829|PDB:2V9L"
FT TURN 132..134
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 138..142
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 145..150
FT /evidence="ECO:0007829|PDB:2V9L"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 158..167
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 172..175
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 180..182
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 188..190
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 191..201
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 205..209
FT /evidence="ECO:0007829|PDB:2V9L"
FT TURN 210..212
FT /evidence="ECO:0007829|PDB:2V9L"
FT STRAND 213..220
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 221..243
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 256..263
FT /evidence="ECO:0007829|PDB:2V9L"
FT HELIX 269..272
FT /evidence="ECO:0007829|PDB:2V9L"
SQ SEQUENCE 274 AA; 30145 MW; F9FF0BE156F4E63D CRC64;
MQNITQSWFV QGMIKATTDA WLKGWDERNG GNLTLRLDDA DIAPYHDNFH QQPRYIPLSQ
PMPLLANTPF IVTGSGKFFR NVQLDPAANL GIVKVDSDGA GYHILWGLTN EAVPTSELPA
HFLSHCERIK ATNGKDRVIM HCHATNLIAL TYVLENDTAV FTRQLWEGST ECLVVFPDGV
GILPWMVPGT DEIGQATAQE MQKHSLVLWP FHGVFGSGPT LDETFGLIDT AEKSAQVLVK
VYSMGGMKQT ISREELIALG KRFGVTPLAS ALAL
