RPIB_MYCTU
ID RPIB_MYCTU Reviewed; 162 AA.
AC P9WKD7; L0TCF4; Q79FD7; Q7D737;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 46.
DE RecName: Full=Ribose-5-phosphate isomerase B {ECO:0000303|PubMed:18640127};
DE EC=5.3.1.6 {ECO:0000269|PubMed:14687575, ECO:0000269|PubMed:18640127};
DE AltName: Full=Phosphoriboisomerase B {ECO:0000303|PubMed:18640127};
GN Name=rpiB {ECO:0000303|PubMed:18640127}; OrderedLocusNames=Rv2465c;
GN ORFNames=MTV008.21c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.88 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, AND SUBUNIT.
RX PubMed=14687575; DOI=10.1016/j.jmb.2003.11.021;
RA Roos A.K., Andersson C.E., Bergfors T., Jacobsson M., Karlen A., Unge T.,
RA Jones T.A., Mowbray S.L.;
RT "Mycobacterium tuberculosis ribose-5-phosphate isomerase has a known fold,
RT but a novel active site.";
RL J. Mol. Biol. 335:799-809(2004).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS,
RP SUBUNIT, AND ACTIVE SITE.
RX PubMed=15590681; DOI=10.1074/jbc.m412018200;
RA Roos A.K., Burgos E., Ericsson D.J., Salmon L., Mowbray S.L.;
RT "Competitive inhibitors of Mycobacterium tuberculosis ribose-5-phosphate
RT isomerase B reveal new information about the reaction mechanism.";
RL J. Biol. Chem. 280:6416-6422(2005).
RN [5] {ECO:0007744|PDB:2VVO, ECO:0007744|PDB:2VVP, ECO:0007744|PDB:2VVQ}
RP X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) IN COMPLEX WITH RIBULOSE-5-PHOSPHATE
RP AND SUBSTRATE ANALOGS, FUNCTION, SUBUNIT, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, AND ACTIVE SITE.
RX PubMed=18640127; DOI=10.1016/j.jmb.2008.06.090;
RA Roos A.K., Mariano S., Kowalinski E., Salmon L., Mowbray S.L.;
RT "D-ribose-5-phosphate isomerase B from Escherichia coli is also a
RT functional D-allose-6-phosphate isomerase, while the Mycobacterium
RT tuberculosis enzyme is not.";
RL J. Mol. Biol. 382:667-679(2008).
CC -!- FUNCTION: Catalyzes the interconversion of ribulose-5-P and ribose-5-P.
CC It has not isomerase activity towards D-allose 6-phosphate.
CC {ECO:0000269|PubMed:14687575, ECO:0000269|PubMed:18640127}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=aldehydo-D-ribose 5-phosphate = D-ribulose 5-phosphate;
CC Xref=Rhea:RHEA:14657, ChEBI:CHEBI:58121, ChEBI:CHEBI:58273;
CC EC=5.3.1.6; Evidence={ECO:0000269|PubMed:14687575,
CC ECO:0000269|PubMed:18640127};
CC -!- ACTIVITY REGULATION: Weakly inhibited by phosphate and completely
CC inhibited by iodoacetate. {ECO:0000269|PubMed:14687575}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.0 mM for D-ribose 5-phosphate {ECO:0000269|PubMed:18640127};
CC KM=3.7 mM for D-ribose 5-phosphate {ECO:0000269|PubMed:14687575};
CC Note=kcat is 120 sec(-1) for D-ribose 5-phosphate.
CC {ECO:0000269|PubMed:14687575};
CC -!- PATHWAY: Carbohydrate degradation; pentose phosphate pathway; D-ribose
CC 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage): step
CC 1/1. {ECO:0000305|PubMed:18640127}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:14687575,
CC ECO:0000305|PubMed:15590681, ECO:0000305|PubMed:18640127}.
CC -!- MISCELLANEOUS: In mycobacterial enzymes, the usual proton acceptor is
CC not a cysteine, but is remplaced by a glutamate.
CC {ECO:0000269|PubMed:14687575}.
CC -!- SIMILARITY: Belongs to the LacAB/RpiB family. {ECO:0000305}.
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DR EMBL; AL123456; CCP45258.1; -; Genomic_DNA.
DR RefSeq; WP_003899332.1; NC_000962.3.
DR RefSeq; YP_177884.1; NC_000962.3.
DR PDB; 1USL; X-ray; 1.88 A; A/B/C/D/E=1-162.
DR PDB; 2BES; X-ray; 2.10 A; A/B/C/D/E=1-162.
DR PDB; 2BET; X-ray; 2.20 A; A/B/C/D/E=1-162.
DR PDB; 2VVO; X-ray; 1.85 A; A/B/C/D/E=1-162.
DR PDB; 2VVP; X-ray; 1.65 A; A/B/C/D/E=1-162.
DR PDB; 2VVQ; X-ray; 2.00 A; A/B/C/D/E=1-162.
DR PDBsum; 1USL; -.
DR PDBsum; 2BES; -.
DR PDBsum; 2BET; -.
DR PDBsum; 2VVO; -.
DR PDBsum; 2VVP; -.
DR PDBsum; 2VVQ; -.
DR AlphaFoldDB; P9WKD7; -.
DR SMR; P9WKD7; -.
DR STRING; 83332.Rv2465c; -.
DR BindingDB; P9WKD7; -.
DR ChEMBL; CHEMBL1770044; -.
DR DrugBank; DB03108; 4-phospho-D-erythronic acid.
DR DrugBank; DB04496; 4-Phospho-D-erythronohydroxamic acid.
DR PaxDb; P9WKD7; -.
DR DNASU; 887225; -.
DR GeneID; 887225; -.
DR KEGG; mtu:Rv2465c; -.
DR PATRIC; fig|83332.111.peg.2759; -.
DR TubercuList; Rv2465c; -.
DR eggNOG; COG0698; Bacteria.
DR OMA; DYPPFCL; -.
DR PhylomeDB; P9WKD7; -.
DR BRENDA; 5.3.1.6; 3445.
DR SABIO-RK; P9WKD7; -.
DR UniPathway; UPA00115; UER00412.
DR PRO; PR:P9WKD7; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005576; C:extracellular region; HDA:MTBBASE.
DR GO; GO:0016853; F:isomerase activity; IBA:GO_Central.
DR GO; GO:0004751; F:ribose-5-phosphate isomerase activity; IDA:MTBBASE.
DR GO; GO:0019316; P:D-allose catabolic process; IBA:GO_Central.
DR GO; GO:0009052; P:pentose-phosphate shunt, non-oxidative branch; IDA:MTBBASE.
DR Gene3D; 3.40.1400.10; -; 1.
DR InterPro; IPR011860; Rib-5-P_Isoase_Actino.
DR InterPro; IPR003500; RpiB_LacA_LacB.
DR InterPro; IPR036569; RpiB_LacA_LacB_sf.
DR PANTHER; PTHR30345; PTHR30345; 1.
DR Pfam; PF02502; LacAB_rpiB; 1.
DR PIRSF; PIRSF005384; RpiB_LacA_B; 1.
DR SUPFAM; SSF89623; SSF89623; 1.
DR TIGRFAMs; TIGR02133; RPI_actino; 1.
DR TIGRFAMs; TIGR00689; rpiB_lacA_lacB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Isomerase; Reference proteome.
FT CHAIN 1..162
FT /note="Ribose-5-phosphate isomerase B"
FT /id="PRO_0000251148"
FT ACT_SITE 75
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:15590681,
FT ECO:0000305|PubMed:18640127, ECO:0007744|PDB:2BES,
FT ECO:0007744|PDB:2BET, ECO:0007744|PDB:2VVO,
FT ECO:0007744|PDB:2VVP, ECO:0007744|PDB:2VVQ"
FT ACT_SITE 102
FT /note="Proton donor"
FT /evidence="ECO:0000305|PubMed:15590681,
FT ECO:0000305|PubMed:18640127, ECO:0007744|PDB:2BES,
FT ECO:0007744|PDB:2BET, ECO:0007744|PDB:2VVO,
FT ECO:0007744|PDB:2VVP, ECO:0007744|PDB:2VVQ"
FT BINDING 11..12
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:14687575,
FT ECO:0000269|PubMed:15590681, ECO:0000269|PubMed:18640127,
FT ECO:0007744|PDB:1USL, ECO:0007744|PDB:2BES,
FT ECO:0007744|PDB:2BET, ECO:0007744|PDB:2VVO,
FT ECO:0007744|PDB:2VVP, ECO:0007744|PDB:2VVQ"
FT BINDING 70..74
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:15590681,
FT ECO:0000269|PubMed:18640127, ECO:0007744|PDB:2BES,
FT ECO:0007744|PDB:2BET, ECO:0007744|PDB:2VVO,
FT ECO:0007744|PDB:2VVP, ECO:0007744|PDB:2VVQ"
FT BINDING 103
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:15590681,
FT ECO:0000269|PubMed:18640127, ECO:0007744|PDB:2BET,
FT ECO:0007744|PDB:2VVO, ECO:0007744|PDB:2VVP"
FT BINDING 113
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:14687575,
FT ECO:0000269|PubMed:15590681, ECO:0000269|PubMed:18640127,
FT ECO:0007744|PDB:1USL, ECO:0007744|PDB:2BES,
FT ECO:0007744|PDB:2BET, ECO:0007744|PDB:2VVO,
FT ECO:0007744|PDB:2VVP, ECO:0007744|PDB:2VVQ"
FT BINDING 137
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:14687575,
FT ECO:0000269|PubMed:15590681, ECO:0000269|PubMed:18640127,
FT ECO:0007744|PDB:1USL, ECO:0007744|PDB:2BES,
FT ECO:0007744|PDB:2BET, ECO:0007744|PDB:2VVO,
FT ECO:0007744|PDB:2VVP, ECO:0007744|PDB:2VVQ"
FT BINDING 141
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000269|PubMed:14687575,
FT ECO:0000269|PubMed:18640127, ECO:0007744|PDB:1USL,
FT ECO:0007744|PDB:2VVO, ECO:0007744|PDB:2VVP,
FT ECO:0007744|PDB:2VVQ"
FT STRAND 5..10
FT /evidence="ECO:0007829|PDB:2VVP"
FT HELIX 12..27
FT /evidence="ECO:0007829|PDB:2VVP"
FT STRAND 31..34
FT /evidence="ECO:0007829|PDB:2VVP"
FT HELIX 47..59
FT /evidence="ECO:0007829|PDB:2VVP"
FT STRAND 64..72
FT /evidence="ECO:0007829|PDB:2VVP"
FT HELIX 73..80
FT /evidence="ECO:0007829|PDB:2VVP"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:2VVP"
FT HELIX 93..101
FT /evidence="ECO:0007829|PDB:2VVP"
FT STRAND 106..111
FT /evidence="ECO:0007829|PDB:2VVP"
FT HELIX 112..114
FT /evidence="ECO:0007829|PDB:2VVP"
FT HELIX 117..129
FT /evidence="ECO:0007829|PDB:2VVP"
FT HELIX 136..151
FT /evidence="ECO:0007829|PDB:2VVP"
SQ SEQUENCE 162 AA; 17278 MW; 31EF834F28783E00 CRC64;
MSGMRVYLGA DHAGYELKQR IIEHLKQTGH EPIDCGALRY DADDDYPAFC IAAATRTVAD
PGSLGIVLGG SGNGEQIAAN KVPGARCALA WSVQTAALAR EHNNAQLIGI GGRMHTVAEA
LAIVDAFVTT PWSKAQRHQR RIDILAEYER THEAPPVPGA PA
