RIBA_ECOLI
ID RIBA_ECOLI Reviewed; 196 AA.
AC P0A7I7; P25523; P78147;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=GTP cyclohydrolase-2;
DE EC=3.5.4.25 {ECO:0000269|PubMed:8320220};
DE AltName: Full=GTP cyclohydrolase II;
GN Name=ribA; OrderedLocusNames=b1277, JW1269;
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 1-13, AND CATALYTIC
RP ACTIVITY.
RC STRAIN=K12;
RX PubMed=8320220; DOI=10.1128/jb.175.13.4045-4051.1993;
RA Richter G., Ritz H., Katzenmeier G., Volk R., Kohnle A., Lottspeich F.,
RA Allendorf D., Bacher A.;
RT "Biosynthesis of riboflavin: cloning, sequencing, mapping, and expression
RT of the gene coding for GTP cyclohydrolase II in Escherichia coli.";
RL J. Bacteriol. 175:4045-4051(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9097039; DOI=10.1093/dnares/3.6.363;
RA Aiba H., Baba T., Fujita K., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kasai H., Kashimoto K., Kimura S., Kitakawa M., Kitagawa M., Makino K.,
RA Miki T., Mizobuchi K., Mori H., Mori T., Motomura K., Nakade S.,
RA Nakamura Y., Nashimoto H., Nishio Y., Oshima T., Saito N., Sampei G.,
RA Seki Y., Sivasundaram S., Tagami H., Takeda J., Takemoto K., Takeuchi Y.,
RA Wada C., Yamamoto Y., Horiuchi T.;
RT "A 570-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 28.0-40.1 min region on the linkage map.";
RL DNA Res. 3:363-377(1996).
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 107-196.
RX PubMed=1541275; DOI=10.1111/j.1432-1033.1992.tb16673.x;
RA Prodromou C., Artymiuk P.J., Guest J.R.;
RT "The aconitase of Escherichia coli. Nucleotide sequence of the aconitase
RT gene and amino acid sequence similarity with mitochondrial aconitases, the
RT iron-responsive-element-binding protein and isopropylmalate isomerases.";
RL Eur. J. Biochem. 204:599-609(1992).
RN [6]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, ACTIVITY REGULATION, AND
RP COFACTOR.
RX PubMed=235552; DOI=10.1016/s0021-9258(19)41549-4;
RA Foor F., Brown G.M.;
RT "Purification and properties of guanosine triphosphate cyclohydrolase II
RT from Escherichia coli.";
RL J. Biol. Chem. 250:3545-3551(1975).
RN [7]
RP ENZYME MECHANISM, AND ACTIVITY REGULATION.
RX PubMed=11301327; DOI=10.1074/jbc.m100752200;
RA Ritz H., Schramek N., Bracher A., Herz S., Eisenreich W., Richter G.,
RA Bacher A.;
RT "Biosynthesis of riboflavin: studies on the mechanism of GTP cyclohydrolase
RT II.";
RL J. Biol. Chem. 276:22273-22277(2001).
RN [8]
RP COFACTOR, AND MUTAGENESIS OF CYS-54; CYS-65 AND CYS-67.
RX PubMed=12392559; DOI=10.1046/j.1432-1033.2002.03239.x;
RA Kaiser J., Schramek N., Eberhardt S., Puettmer S., Schuster M., Bacher A.;
RT "Biosynthesis of vitamin B2.";
RL Eur. J. Biochem. 269:5264-5270(2002).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (1.54 ANGSTROMS) OF APOENZYME AND IN COMPLEX WITH GTP
RP ANALOG AND ZINC IONS, AND REACTION MECHANISM.
RX PubMed=16115872; DOI=10.1074/jbc.m507725200;
RA Ren J., Kotaka M., Lockyer M., Lamb H.K., Hawkins A.R., Stammers D.K.;
RT "GTP cyclohydrolase II structure and mechanism.";
RL J. Biol. Chem. 280:36912-36919(2005).
CC -!- FUNCTION: Catalyzes the conversion of GTP to 2,5-diamino-6-
CC ribosylamino-4(3H)-pyrimidinone 5'-phosphate (DARP), formate and
CC pyrophosphate. {ECO:0000269|PubMed:235552}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=GTP + 4 H2O = 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-
CC pyrimidine + formate + 3 H(+) + 2 phosphate; Xref=Rhea:RHEA:23704,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:15740,
CC ChEBI:CHEBI:37565, ChEBI:CHEBI:43474, ChEBI:CHEBI:58614; EC=3.5.4.25;
CC Evidence={ECO:0000269|PubMed:8320220};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12392559, ECO:0000269|PubMed:235552};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|PubMed:12392559,
CC ECO:0000269|PubMed:235552};
CC -!- ACTIVITY REGULATION: Competitively inhibited by pyrophosphate.
CC {ECO:0000269|PubMed:11301327, ECO:0000269|PubMed:235552}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=41 uM for GTP {ECO:0000269|PubMed:235552};
CC pH dependence:
CC Optimum pH is 8.5. {ECO:0000269|PubMed:235552};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 1/4.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:16115872,
CC ECO:0000269|PubMed:235552}.
CC -!- INTERACTION:
CC P0A7I7; P08244: pyrF; NbExp=2; IntAct=EBI-1123314, EBI-1123202;
CC -!- MISCELLANEOUS: Catalyzes the formation of GMP as minor product, with
CC concomitant release of pyrophosphate. Release of pyrophosphate requires
CC magnesium ions.
CC -!- SIMILARITY: Belongs to the GTP cyclohydrolase II family. {ECO:0000305}.
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DR EMBL; X67876; CAA48075.1; -; Genomic_DNA.
DR EMBL; U00096; AAC74359.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA14831.1; -; Genomic_DNA.
DR EMBL; X60293; CAA42835.1; -; Genomic_DNA.
DR PIR; A40654; A40654.
DR RefSeq; NP_415793.1; NC_000913.3.
DR RefSeq; WP_001176295.1; NZ_STEB01000005.1.
DR PDB; 2BZ0; X-ray; 2.60 A; A/B=1-196.
DR PDB; 2BZ1; X-ray; 1.54 A; A=1-196.
DR PDBsum; 2BZ0; -.
DR PDBsum; 2BZ1; -.
DR AlphaFoldDB; P0A7I7; -.
DR SMR; P0A7I7; -.
DR BioGRID; 4263359; 47.
DR DIP; DIP-36049N; -.
DR IntAct; P0A7I7; 2.
DR STRING; 511145.b1277; -.
DR jPOST; P0A7I7; -.
DR PaxDb; P0A7I7; -.
DR PRIDE; P0A7I7; -.
DR EnsemblBacteria; AAC74359; AAC74359; b1277.
DR EnsemblBacteria; BAA14831; BAA14831; BAA14831.
DR GeneID; 66674898; -.
DR GeneID; 945763; -.
DR KEGG; ecj:JW1269; -.
DR KEGG; eco:b1277; -.
DR PATRIC; fig|1411691.4.peg.1004; -.
DR EchoBASE; EB1307; -.
DR eggNOG; COG0807; Bacteria.
DR HOGENOM; CLU_020273_2_1_6; -.
DR InParanoid; P0A7I7; -.
DR OMA; GQGFILY; -.
DR PhylomeDB; P0A7I7; -.
DR BioCyc; EcoCyc:GTP-CYCLOHYDRO-II-MON; -.
DR BioCyc; MetaCyc:GTP-CYCLOHYDRO-II-MON; -.
DR BRENDA; 3.5.4.25; 2026.
DR SABIO-RK; P0A7I7; -.
DR UniPathway; UPA00275; UER00400.
DR EvolutionaryTrace; P0A7I7; -.
DR PRO; PR:P0A7I7; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003935; F:GTP cyclohydrolase II activity; IDA:EcoCyc.
DR GO; GO:0000287; F:magnesium ion binding; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IMP:EcoCyc.
DR CDD; cd00641; GTP_cyclohydro2; 1.
DR Gene3D; 3.40.50.10990; -; 1.
DR HAMAP; MF_00179; RibA; 1.
DR InterPro; IPR032677; GTP_cyclohydro_II.
DR InterPro; IPR000926; RibA.
DR InterPro; IPR036144; RibA-like_sf.
DR Pfam; PF00925; GTP_cyclohydro2; 1.
DR SUPFAM; SSF142695; SSF142695; 1.
DR TIGRFAMs; TIGR00505; ribA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; GTP-binding; Hydrolase;
KW Metal-binding; Nucleotide-binding; Reference proteome;
KW Riboflavin biosynthesis; Zinc.
FT CHAIN 1..196
FT /note="GTP cyclohydrolase-2"
FT /id="PRO_0000151754"
FT ACT_SITE 126
FT /note="Proton acceptor"
FT /evidence="ECO:0000255"
FT ACT_SITE 128
FT /note="Nucleophile"
FT BINDING 49..53
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 54
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 65
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 67
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT BINDING 70
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 92..94
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 114
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 149
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT BINDING 154
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT MUTAGEN 54
FT /note="C->S: Loss of zinc binding. Loss of ring-opening
FT activity. Can still remove phosphate from GTP."
FT /evidence="ECO:0000269|PubMed:12392559"
FT MUTAGEN 65
FT /note="C->S: Loss of zinc binding. Loss of ring-opening
FT activity. Can still remove phosphate from GTP."
FT /evidence="ECO:0000269|PubMed:12392559"
FT MUTAGEN 67
FT /note="C->S: Loss of zinc binding. Loss of ring-opening
FT activity. Can still remove phosphate from GTP."
FT /evidence="ECO:0000269|PubMed:12392559"
FT STRAND 3..13
FT /evidence="ECO:0007829|PDB:2BZ1"
FT STRAND 16..25
FT /evidence="ECO:0007829|PDB:2BZ1"
FT TURN 26..28
FT /evidence="ECO:0007829|PDB:2BZ1"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:2BZ1"
FT STRAND 42..44
FT /evidence="ECO:0007829|PDB:2BZ1"
FT STRAND 46..52
FT /evidence="ECO:0007829|PDB:2BZ1"
FT HELIX 55..58
FT /evidence="ECO:0007829|PDB:2BZ1"
FT STRAND 63..66
FT /evidence="ECO:0007829|PDB:2BZ0"
FT HELIX 67..81
FT /evidence="ECO:0007829|PDB:2BZ1"
FT STRAND 83..89
FT /evidence="ECO:0007829|PDB:2BZ1"
FT HELIX 92..95
FT /evidence="ECO:0007829|PDB:2BZ1"
FT HELIX 98..109
FT /evidence="ECO:0007829|PDB:2BZ1"
FT HELIX 114..120
FT /evidence="ECO:0007829|PDB:2BZ1"
FT HELIX 131..139
FT /evidence="ECO:0007829|PDB:2BZ1"
FT STRAND 144..148
FT /evidence="ECO:0007829|PDB:2BZ1"
FT HELIX 152..160
FT /evidence="ECO:0007829|PDB:2BZ1"
FT STRAND 165..169
FT /evidence="ECO:0007829|PDB:2BZ1"
SQ SEQUENCE 196 AA; 21836 MW; C22FED98F48098DF CRC64;
MQLKRVAEAK LPTPWGDFLM VGFEELATGH DHVALVYGDI SGHTPVLARV HSECLTGDAL
FSLRCDCGFQ LEAALTQIAE EGRGILLYHR QEGRNIGLLN KIRAYALQDQ GYDTVEANHQ
LGFAADERDF TLCADMFKLL GVNEVRLLTN NPKKVEILTE AGINIVERVP LIVGRNPNNE
HYLDTKAEKM GHLLNK
