ID   RHAA_ECOLI              Reviewed;         419 AA.
AC   P32170; Q2M8K0; Q6BEY0;
DT   01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT   11-OCT-2004, sequence version 2.
DT   27-MAR-2024, entry version 173.
DE   RecName: Full=L-rhamnose isomerase {ECO:0000255|HAMAP-Rule:MF_00541, ECO:0000303|PubMed:14243758};
DE            Short=RhamIso {ECO:0000303|PubMed:8564401};
DE            EC=5.3.1.14 {ECO:0000255|HAMAP-Rule:MF_00541, ECO:0000269|PubMed:14243758, ECO:0000269|PubMed:1650346, ECO:0000269|PubMed:8564401};
GN   Name=rhaA {ECO:0000255|HAMAP-Rule:MF_00541};
GN   OrderedLocusNames=b3903, JW5561;
OS   Escherichia coli (strain K12).
OC   Bacteria; Pseudomonadota; 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   SEQUENCE REVISION TO 359-360.
RX   PubMed=16397293; DOI=10.1093/nar/gkj405;
RA   Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R.,
RA   Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T.,
RA   Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H.,
RA   Thomson N.R., Wishart D., Wanner B.L.;
RT   "Escherichia coli K-12: a cooperatively developed annotation snapshot
RT   -- 2005.";
RL   Nucleic Acids Res. 34:1-9(2006).
RN   [5]
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   [6]
RP   FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC   STRAIN=B;
RX   PubMed=14243758; DOI=10.1016/0926-6569(64)90263-9;
RA   Takagi Y., Sawada H.;
RT   "The metabolism of L-rhamnose in Escherichia coli. I. L-rhamnose
RT   isomerase.";
RL   Biochim. Biophys. Acta 92:10-17(1964).
RN   [7]
RP   FUNCTION.
RX   PubMed=2558952; DOI=10.1016/0378-1097(89)90226-7;
RA   Badia J., Baldoma L., Aguilar J., Boronat A.;
RT   "Identification of the rhaA, rhaB and rhaD gene products from Escherichia
RT   coli K-12.";
RL   FEMS Microbiol. Lett. 65:253-257(1989).
RN   [8]
RP   FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND INDUCTION.
RC   STRAIN=K12;
RX   PubMed=1650346; DOI=10.1128/jb.173.16.5144-5150.1991;
RA   Badia J., Gimenez R., Baldoma L., Barnes E., Fessner W.D., Aguilar J.;
RT   "L-lyxose metabolism employs the L-rhamnose pathway in mutant cells of
RT   Escherichia coli adapted to grow on L-lyxose.";
RL   J. Bacteriol. 173:5144-5150(1991).
RN   [9]
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   [10]
RP   FUNCTION, AND CATALYTIC ACTIVITY.
RX   PubMed=8564401; DOI=10.1016/0968-0896(95)00119-2;
RA   Garcia-Junceda E., Shen G.J., Alajarin R., Wong C.H.;
RT   "Cloning and overexpression of rhamnose isomerase and fucose isomerase.";
RL   Bioorg. Med. Chem. 3:1349-1355(1995).
RN   [11]
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   [12] {ECO:0007744|PDB:1D8W, ECO:0007744|PDB:1DE5, ECO:0007744|PDB:1DE6}
RP   X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH MANGANESE; ZINC AND
RP   ALDEHYDO-L-RHAMNOSE, COFACTOR, AND SUBUNIT.
RX   PubMed=10891278; DOI=10.1006/jmbi.2000.3896;
RA   Korndoerfer I.P., Fessner W.-D., Matthews B.W.;
RT   "The structure of rhamnose isomerase from Escherichia coli and its relation
RT   with xylose isomerase illustrates a change between inter and intra-subunit
RT   complementation during evolution.";
RL   J. Mol. Biol. 300:917-933(2000).
CC   -!- FUNCTION: Catalyzes the interconversion of L-rhamnose and L-rhamnulose
CC       (PubMed:14243758, PubMed:2558952, PubMed:8564401, PubMed:1650346). Can
CC       also catalyze the isomerization of L-lyxose to L-xylulose
CC       (PubMed:1650346). {ECO:0000269|PubMed:14243758,
CC       ECO:0000269|PubMed:1650346, ECO:0000269|PubMed:2558952,
CC       ECO:0000269|PubMed:8564401}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L-rhamnopyranose = L-rhamnulose; Xref=Rhea:RHEA:23160,
CC         ChEBI:CHEBI:17897, ChEBI:CHEBI:62346; EC=5.3.1.14;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00541,
CC         ECO:0000269|PubMed:14243758, ECO:0000269|PubMed:1650346,
CC         ECO:0000269|PubMed:8564401};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L-lyxopyranose = L-xylulose; Xref=Rhea:RHEA:28058,
CC         ChEBI:CHEBI:17399, ChEBI:CHEBI:62321;
CC         Evidence={ECO:0000269|PubMed:1650346};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00541, ECO:0000269|PubMed:10891278,
CC         ECO:0000269|PubMed:14243758};
CC       Note=Binds 1 Mn(2+) ion per subunit. {ECO:0000255|HAMAP-Rule:MF_00541,
CC       ECO:0000269|PubMed:10891278};
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=2 mM for L-rhamnose {ECO:0000269|PubMed:14243758,
CC         ECO:0000269|PubMed:1650346};
CC         KM=5 mM for L-lyxose {ECO:0000269|PubMed:1650346};
CC         KM=1.7 mM for L-rhamnulose {ECO:0000269|PubMed:14243758};
CC         Vmax=6.2 umol/min/mg enzyme with L-rhamnose as substrate
CC         {ECO:0000269|PubMed:1650346};
CC         Vmax=6 umol/min/mg enzyme with L-lyxose as substrate
CC         {ECO:0000269|PubMed:1650346};
CC       pH dependence:
CC         Optimum pH is 7.6. {ECO:0000269|PubMed:14243758};
CC   -!- PATHWAY: Carbohydrate degradation; L-rhamnose degradation; glycerone
CC       phosphate from L-rhamnose: step 1/3. {ECO:0000255|HAMAP-Rule:MF_00541,
CC       ECO:0000305|PubMed:2558952}.
CC   -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_00541,
CC       ECO:0000269|PubMed:10891278}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00541,
CC       ECO:0000305}.
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 (PubMed:10852886, PubMed:8230210). Also induced by L-lyxose
CC       (PubMed:1650346). {ECO:0000269|PubMed:10852886,
CC       ECO:0000269|PubMed:1650346, ECO:0000269|PubMed:8230210}.
CC   -!- MISCELLANEOUS: In the crystal structure, RhaA appears to bind a zinc
CC       ion at a structural site. However, the metal ion may be different in
CC       vivo.
CC   -!- SIMILARITY: Belongs to the rhamnose isomerase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00541, ECO:0000305}.
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DR   EMBL; X60472; CAA43002.1; -; Genomic_DNA.
DR   EMBL; L19201; AAB03036.1; -; Genomic_DNA.
DR   EMBL; U00096; AAT48234.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE77406.1; -; Genomic_DNA.
DR   PIR; S40847; S40847.
DR   RefSeq; WP_001311268.1; NZ_SSZK01000014.1.
DR   RefSeq; YP_026276.1; NC_000913.3.
DR   PDB; 1D8W; X-ray; 1.60 A; A/B/C/D=1-419.
DR   PDB; 1DE5; X-ray; 2.20 A; A/B/C/D=1-419.
DR   PDB; 1DE6; X-ray; 2.10 A; A/B/C/D=1-419.
DR   PDBsum; 1D8W; -.
DR   PDBsum; 1DE5; -.
DR   PDBsum; 1DE6; -.
DR   AlphaFoldDB; P32170; -.
DR   SMR; P32170; -.
DR   DIP; DIP-10690N; -.
DR   STRING; 511145.b3903; -.
DR   DrugBank; DB02399; L-Rhamnitol.
DR   DrugBank; DB02961; Rhamnose.
DR   PaxDb; 511145-b3903; -.
DR   EnsemblBacteria; AAT48234; AAT48234; b3903.
DR   GeneID; 948400; -.
DR   KEGG; ecj:JW5561; -.
DR   KEGG; eco:b3903; -.
DR   PATRIC; fig|1411691.4.peg.2803; -.
DR   EchoBASE; EB1813; -.
DR   eggNOG; COG4806; Bacteria.
DR   HOGENOM; CLU_052790_0_0_6; -.
DR   InParanoid; P32170; -.
DR   OMA; SIHCWQG; -.
DR   OrthoDB; 9766697at2; -.
DR   PhylomeDB; P32170; -.
DR   BioCyc; EcoCyc:RHAMNISOM-MONOMER; -.
DR   BioCyc; MetaCyc:RHAMNISOM-MONOMER; -.
DR   BRENDA; 5.3.1.14; 2026.
DR   UniPathway; UPA00541; UER00601.
DR   EvolutionaryTrace; P32170; -.
DR   PRO; PR:P32170; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0032991; C:protein-containing complex; IDA:CAFA.
DR   GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR   GO; GO:0008740; F:L-rhamnose isomerase activity; IDA:EcoCyc.
DR   GO; GO:0030145; F:manganese ion binding; IDA:CAFA.
DR   GO; GO:0033296; F:rhamnose binding; IDA:CAFA.
DR   GO; GO:0008270; F:zinc ion binding; IDA:CAFA.
DR   GO; GO:0019324; P:L-lyxose metabolic process; IEP:EcoCyc.
DR   GO; GO:0051289; P:protein homotetramerization; IDA:EcoCyc.
DR   GO; GO:0019301; P:rhamnose catabolic process; IMP:EcoCyc.
DR   DisProt; DP00429; -.
DR   Gene3D; 3.20.20.150; Divalent-metal-dependent TIM barrel enzymes; 1.
DR   HAMAP; MF_00541; RhaA; 1.
DR   InterPro; IPR009308; Rhamnose_isomerase.
DR   InterPro; IPR036237; Xyl_isomerase-like_sf.
DR   NCBIfam; TIGR01748; rhaA; 1.
DR   PANTHER; PTHR30268; L-RHAMNOSE ISOMERASE; 1.
DR   PANTHER; PTHR30268:SF0; L-RHAMNOSE ISOMERASE; 1.
DR   Pfam; PF06134; RhaA; 1.
DR   SUPFAM; SSF51658; Xylose isomerase-like; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; Isomerase; Manganese; Metal-binding;
KW   Reference proteome; Rhamnose metabolism; Zinc.
FT   CHAIN           1..419
FT                   /note="L-rhamnose isomerase"
FT                   /id="PRO_0000090552"
FT   BINDING         95
FT                   /ligand="L-rhamnose"
FT                   /ligand_id="ChEBI:CHEBI:16055"
FT                   /evidence="ECO:0000269|PubMed:10891278,
FT                   ECO:0007744|PDB:1DE6"
FT   BINDING         226..228
FT                   /ligand="L-rhamnose"
FT                   /ligand_id="ChEBI:CHEBI:16055"
FT                   /evidence="ECO:0000269|PubMed:10891278,
FT                   ECO:0007744|PDB:1DE6"
FT   BINDING         226
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000269|PubMed:10891278,
FT                   ECO:0007744|PDB:1D8W, ECO:0007744|PDB:1DE5,
FT                   ECO:0007744|PDB:1DE6"
FT   BINDING         259
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000269|PubMed:10891278,
FT                   ECO:0007744|PDB:1D8W, ECO:0007744|PDB:1DE5,
FT                   ECO:0007744|PDB:1DE6"
FT   BINDING         262
FT                   /ligand="L-rhamnose"
FT                   /ligand_id="ChEBI:CHEBI:16055"
FT                   /evidence="ECO:0000269|PubMed:10891278,
FT                   ECO:0007744|PDB:1DE6"
FT   BINDING         262
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00541,
FT                   ECO:0000269|PubMed:10891278, ECO:0007744|PDB:1DE6"
FT   BINDING         286
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000269|PubMed:10891278,
FT                   ECO:0007744|PDB:1D8W, ECO:0007744|PDB:1DE5,
FT                   ECO:0007744|PDB:1DE6"
FT   BINDING         294
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00541,
FT                   ECO:0000269|PubMed:10891278, ECO:0007744|PDB:1DE6"
FT   BINDING         296
FT                   /ligand="Mn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29035"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00541,
FT                   ECO:0000269|PubMed:10891278, ECO:0007744|PDB:1DE6"
FT   BINDING         326
FT                   /ligand="L-rhamnose"
FT                   /ligand_id="ChEBI:CHEBI:16055"
FT                   /evidence="ECO:0000269|PubMed:10891278,
FT                   ECO:0007744|PDB:1DE6"
FT   BINDING         326
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000269|PubMed:10891278,
FT                   ECO:0007744|PDB:1D8W, ECO:0007744|PDB:1DE5,
FT                   ECO:0007744|PDB:1DE6"
FT   CONFLICT        359..360
FT                   /note="EL -> DV (in Ref. 2; AAB03036)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        366
FT                   /note="A -> P (in Ref. 1; CAA43002)"
FT                   /evidence="ECO:0000305"
FT   HELIX           4..18
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           23..30
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          35..38
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           39..42
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   TURN            43..45
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          48..53
FT                   /evidence="ECO:0007829|PDB:1DE6"
FT   HELIX           72..84
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          90..95
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           96..98
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           107..109
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           112..115
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           116..124
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          128..132
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          136..138
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           139..141
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           152..176
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          180..184
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          189..192
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           198..211
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   TURN            218..220
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          221..226
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          236..240
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           242..252
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          255..259
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           269..276
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   TURN            277..279
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          283..287
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          291..294
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           303..314
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   TURN            318..320
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   STRAND          321..325
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           334..353
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           357..364
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   TURN            365..367
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           369..379
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           384..394
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   HELIX           403..413
FT                   /evidence="ECO:0007829|PDB:1D8W"
FT   TURN            414..416
FT                   /evidence="ECO:0007829|PDB:1D8W"
SQ   SEQUENCE   419 AA;  47199 MW;  D237E95BD24999BA CRC64;
     MTTQLEQAWE LAKQRFAAVG IDVEEALRQL DRLPVSMHCW QGDDVSGFEN PEGSLTGGIQ
     ATGNYPGKAR NASELRADLE QAMRLIPGPK RLNLHAIYLE SDTPVSRDQI KPEHFKNWVE
     WAKANQLGLD FNPSCFSHPL SADGFTLSHA DDSIRQFWID HCKASRRVSA YFGEQLGTPS
     VMNIWIPDGM KDITVDRLAP RQRLLAALDE VISEKLNPAH HIDAVESKLF GIGAESYTVG
     SNEFYMGYAT SRQTALCLDA GHFHPTEVIS DKISAAMLYV PQLLLHVSRP VRWDSDHVVL
     LDDETQAIAS EIVRHDLFDR VHIGLDFFDA SINRIAAWVI GTRNMKKALL RALLEPTAEL
     RKLEAAGDYT ARLALLEEQK SLPWQAVWEM YCQRHDTPAG SEWLESVRAY EKEILSRRG
//