RIBBA_MYCTA
ID RIBBA_MYCTA Reviewed; 425 AA.
AC A5U2B7;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 10-JUL-2007, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=Riboflavin biosynthesis protein RibBA {ECO:0000255|HAMAP-Rule:MF_01283};
DE Includes:
DE RecName: Full=3,4-dihydroxy-2-butanone 4-phosphate synthase {ECO:0000255|HAMAP-Rule:MF_01283};
DE Short=DHBP synthase {ECO:0000255|HAMAP-Rule:MF_01283};
DE EC=4.1.99.12 {ECO:0000255|HAMAP-Rule:MF_01283};
DE Includes:
DE RecName: Full=GTP cyclohydrolase-2 {ECO:0000255|HAMAP-Rule:MF_01283};
DE EC=3.5.4.25 {ECO:0000255|HAMAP-Rule:MF_01283};
DE AltName: Full=GTP cyclohydrolase II {ECO:0000255|HAMAP-Rule:MF_01283};
GN Name=ribBA {ECO:0000255|HAMAP-Rule:MF_01283}; OrderedLocusNames=MRA_1424;
OS Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=419947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25177 / H37Ra;
RX PubMed=18584054; DOI=10.1371/journal.pone.0002375;
RA Zheng H., Lu L., Wang B., Pu S., Zhang X., Zhu G., Shi W., Zhang L.,
RA Wang H., Wang S., Zhao G., Zhang Y.;
RT "Genetic basis of virulence attenuation revealed by comparative genomic
RT analysis of Mycobacterium tuberculosis strain H37Ra versus H37Rv.";
RL PLoS ONE 3:E2375-E2375(2008).
CC -!- FUNCTION: Catalyzes the conversion of D-ribulose 5-phosphate to formate
CC and 3,4-dihydroxy-2-butanone 4-phosphate. {ECO:0000255|HAMAP-
CC Rule:MF_01283}.
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:0000255|HAMAP-Rule:MF_01283}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribulose 5-phosphate = (2S)-2-hydroxy-3-oxobutyl phosphate +
CC formate + H(+); Xref=Rhea:RHEA:18457, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:15740, ChEBI:CHEBI:58121, ChEBI:CHEBI:58830;
CC EC=4.1.99.12; Evidence={ECO:0000255|HAMAP-Rule:MF_01283};
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:0000255|HAMAP-Rule:MF_01283};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01283};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01283};
CC Note=Binds 2 divalent metal cations per subunit. Magnesium or
CC manganese. {ECO:0000255|HAMAP-Rule:MF_01283};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01283};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01283};
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 2-hydroxy-3-
CC oxobutyl phosphate from D-ribulose 5-phosphate: step 1/1.
CC {ECO:0000255|HAMAP-Rule:MF_01283}.
CC -!- PATHWAY: Cofactor biosynthesis; riboflavin biosynthesis; 5-amino-6-(D-
CC ribitylamino)uracil from GTP: step 1/4. {ECO:0000255|HAMAP-
CC Rule:MF_01283}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the DHBP synthase
CC family. {ECO:0000255|HAMAP-Rule:MF_01283}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the GTP
CC cyclohydrolase II family. {ECO:0000255|HAMAP-Rule:MF_01283}.
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DR EMBL; CP000611; ABQ73167.1; -; Genomic_DNA.
DR RefSeq; WP_003407334.1; NZ_CP016972.1.
DR PDB; 3MGZ; X-ray; 2.07 A; A=1-206.
DR PDB; 3MIO; X-ray; 1.80 A; A/B=1-206.
DR PDB; 3MK5; X-ray; 2.06 A; A=1-206.
DR PDB; 4I14; X-ray; 3.00 A; A/B=1-425.
DR PDBsum; 3MGZ; -.
DR PDBsum; 3MIO; -.
DR PDBsum; 3MK5; -.
DR PDBsum; 4I14; -.
DR AlphaFoldDB; A5U2B7; -.
DR SMR; A5U2B7; -.
DR STRING; 419947.MRA_1424; -.
DR EnsemblBacteria; ABQ73167; ABQ73167; MRA_1424.
DR KEGG; mra:MRA_1424; -.
DR eggNOG; COG0108; Bacteria.
DR eggNOG; COG0807; Bacteria.
DR HOGENOM; CLU_020273_1_2_11; -.
DR OMA; ECRGLIC; -.
DR OrthoDB; 900513at2; -.
DR BRENDA; 4.1.99.12; 3445.
DR UniPathway; UPA00275; UER00399.
DR UniPathway; UPA00275; UER00400.
DR EvolutionaryTrace; A5U2B7; -.
DR Proteomes; UP000001988; Chromosome.
DR GO; GO:0008686; F:3,4-dihydroxy-2-butanone-4-phosphate synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-KW.
DR GO; GO:0003935; F:GTP cyclohydrolase II activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0030145; F:manganese ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009231; P:riboflavin biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd00641; GTP_cyclohydro2; 1.
DR Gene3D; 3.40.50.10990; -; 1.
DR HAMAP; MF_00179; RibA; 1.
DR HAMAP; MF_00180; RibB; 1.
DR HAMAP; MF_01283; RibBA; 1.
DR InterPro; IPR017945; DHBP_synth_RibB-like_a/b_dom.
DR InterPro; IPR000422; DHBP_synthase_RibB.
DR InterPro; IPR032677; GTP_cyclohydro_II.
DR InterPro; IPR000926; RibA.
DR InterPro; IPR036144; RibA-like_sf.
DR InterPro; IPR016299; Riboflavin_synth_RibBA.
DR Pfam; PF00926; DHBP_synthase; 1.
DR Pfam; PF00925; GTP_cyclohydro2; 1.
DR SUPFAM; SSF142695; SSF142695; 1.
DR SUPFAM; SSF55821; SSF55821; 1.
DR TIGRFAMs; TIGR00505; ribA; 1.
DR TIGRFAMs; TIGR00506; ribB; 1.
PE 1: Evidence at protein level;
KW 3D-structure; GTP-binding; Hydrolase; Lyase; Magnesium; Manganese;
KW Metal-binding; Multifunctional enzyme; Nucleotide-binding;
KW Riboflavin biosynthesis; Zinc.
FT CHAIN 1..425
FT /note="Riboflavin biosynthesis protein RibBA"
FT /id="PRO_1000067426"
FT REGION 1..204
FT /note="DHBP synthase"
FT REGION 205..425
FT /note="GTP cyclohydrolase II"
FT ACT_SITE 337
FT /note="Proton acceptor; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT ACT_SITE 339
FT /note="Nucleophile; for GTP cyclohydrolase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 28..29
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 29
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 29
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 33
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 141..145
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 144
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 165
FT /ligand="D-ribulose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:58121"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 259..263
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 264
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 275
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 277
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 280
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 303..305
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 325
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 360
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT BINDING 365
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT SITE 127
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT SITE 165
FT /note="Essential for DHBP synthase activity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01283"
FT HELIX 7..15
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 20..26
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 33..37
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 38..40
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 43..52
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 53..55
FT /evidence="ECO:0007829|PDB:3MK5"
FT STRAND 58..61
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 63..68
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 90..95
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 102..113
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 119..121
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 122..132
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 137..139
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 144..154
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 159..167
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 169..171
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 178..188
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 191..194
FT /evidence="ECO:0007829|PDB:3MIO"
FT HELIX 195..204
FT /evidence="ECO:0007829|PDB:3MIO"
FT STRAND 209..219
FT /evidence="ECO:0007829|PDB:4I14"
FT STRAND 222..231
FT /evidence="ECO:0007829|PDB:4I14"
FT STRAND 237..244
FT /evidence="ECO:0007829|PDB:4I14"
FT STRAND 255..262
FT /evidence="ECO:0007829|PDB:4I14"
FT HELIX 265..268
FT /evidence="ECO:0007829|PDB:4I14"
FT HELIX 277..291
FT /evidence="ECO:0007829|PDB:4I14"
FT STRAND 294..299
FT /evidence="ECO:0007829|PDB:4I14"
FT HELIX 343..350
FT /evidence="ECO:0007829|PDB:4I14"
FT STRAND 354..359
FT /evidence="ECO:0007829|PDB:4I14"
SQ SEQUENCE 425 AA; 46017 MW; FA7F73868814591F CRC64;
MTRLDSVERA VADIAAGKAV IVIDDEDREN EGDLIFAAEK ATPEMVAFMV RYTSGYLCVP
LDGAICDRLG LLPMYAVNQD KHGTAYTVTV DARNGIGTGI SASDRATTMR LLADPTSVAD
DFTRPGHVVP LRAKDGGVLR RPGHTEAAVD LARMAGLQPA GAICEIVSQK DEGSMAHTDE
LRVFADEHGL ALITIADLIE WRRKHEKHIE RVAEARIPTR HGEFRAIGYT SIYEDVEHVA
LVRGEIAGPN ADGDDVLVRV HSECLTGDVF GSRRCDCGPQ LDAALAMVAR EGRGVVLYMR
GHEGRGIGLM HKLQAYQLQD AGADTVDANL KLGLPADARD YGIGAQILVD LGVRSMRLLT
NNPAKRVGLD GYGLHIIERV PLPVRANAEN IRYLMTKRDK LGHDLAGLDD FHESVHLPGE
FGGAL
