ID YBIB_ECOLI Reviewed; 320 AA. AC P30177; DT 01-APR-1993, integrated into UniProtKB/Swiss-Prot. DT 01-APR-1993, sequence version 1. DT 04-NOV-2026, entry version 164. DE RecName: Full=DNA-binding protein YbiB {ECO:0000305}; GN Name=ybiB; OrderedLocusNames=b0800, JW0785; OS Escherichia coli (strain K12). OC Bacteria; Pseudomonadati; Pseudomonadota; Gammaproteobacteria; OC Enterobacterales; Enterobacteriaceae; Escherichia. OX NCBI_TaxID=83333; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=8037924; DOI=10.1266/jjg.69.1; RA Ohmori H.; RT "Structural analysis of the rhlE gene of Escherichia coli."; RL Jpn. J. Genet. 69:1-12(1994). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911; RX PubMed=8905232; DOI=10.1093/dnares/3.3.137; RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K., RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S., RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H., RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G., RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M., RA Horiuchi T.; RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to RT the 12.7-28.0 min region on the linkage map."; RL DNA Res. 3:137-155(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 PROTEIN SEQUENCE OF 1-9. RC STRAIN=K12; RX PubMed=17895580; DOI=10.1266/ggs.82.291; RA Otsuka Y., Koga M., Iwamoto A., Yonesaki T.; RT "A role of RnlA in the RNase LS activity from Escherichia coli."; RL Genes Genet. Syst. 82:291-299(2007). RN [6] {ECO:0007744|PDB:4MUO} RP X-RAY CRYSTALLOGRAPHY, FUNCTION, DNA-BINDING, SUBUNIT, TRANSCRIPTIONAL RP REGULATION, DOMAIN, AND MUTAGENESIS OF LEU-40 AND ILE-51. RC STRAIN=K12 / MG1655 / ATCC 47076; RX PubMed=26063803; DOI=10.1074/jbc.m114.620575; RA Schneider D., Kaiser W., Stutz C., Holinski A., Mayans O., Babinger P.; RT "YbiB from Escherichia coli, the Defining Member of the Novel TrpD2 Family RT of Prokaryotic DNA-binding Proteins."; RL J. Biol. Chem. 290:19527-19539(2015). RN [7] {ECO:0007744|PDB:8BFR, ECO:0007744|PDB:8BFT} RP X-RAY CRYSTALLOGRAPHY IN COMPLEX WITH OBGE C-TERMINAL REGION, FUNCTION, RP DNA-BINDING, ACTIVITY REGULATION, SUBUNIT, INTERACTION WITH OBGE, RP DISRUPTION PHENOTYPE, DOMAIN, AND MUTAGENESIS OF ARG-92 AND ARG-123. RX PubMed=36864742; DOI=10.1093/nar/gkad127; RA Deckers B., Vercauteren S., De Kock V., Martin C., Lazar T., Herpels P., RA Dewachter L., Verstraeten N., Peeters E., Ballet S., Michiels J., RA Michiels J., Galicia C., Versees W.; RT "YbiB: a novel interactor of the GTPase ObgE."; RL Nucleic Acids Res. 51:3420-3435(2023). CC -!- FUNCTION: DNA-binding protein that may be part of the LexA-controlled CC SOS response (PubMed:26063803). Binds with high affinity to DNA without CC sequence specificity (PubMed:26063803, PubMed:36864742). The difference CC in affinity between single- and double-stranded DNA is minor CC (PubMed:26063803). It also interacts with the GTPase ObgE, but does not CC influence ObgE GTP hydrolysis (PubMed:36864742). It may form a link CC between ObgE and the SOS response (PubMed:36864742). Does not show CC anthranilate phosphoribosyltransferase activity, nucleotide salvage CC activity or nucleoside phosphorylase activity (PubMed:26063803). CC {ECO:0000269|PubMed:26063803, ECO:0000269|PubMed:36864742}. CC -!- ACTIVITY REGULATION: Interaction with ObgE efficiently inhibits binding CC to DNA. {ECO:0000269|PubMed:36864742}. CC -!- SUBUNIT: Homodimer (PubMed:26063803, PubMed:36864742). Interacts with CC the GTPase ObgE (PubMed:36864742). YbiB and ObgE form a 2:2 complex, CC with two ObgE molecules binding to one YbiB homodimer CC (PubMed:36864742). {ECO:0000269|PubMed:26063803, CC ECO:0000269|PubMed:36864742}. CC -!- INDUCTION: Expression is under LexA control and induced by DNA-damaging CC agents (PubMed:26063803). Coexpressed with the DNA helicase DinG CC (PubMed:26063803). {ECO:0000269|PubMed:26063803}. CC -!- DOMAIN: Each monomer consists of an N-terminal alpha-helical domain and CC a C-terminal alpha/beta domain (PubMed:26063803, PubMed:36864742). CC Dimerizes via the N-terminal domain in a head-to-head fashion CC (PubMed:26063803). The homodimer contains two DNA binding sites, but CC only one of them is occupied by DNA due to negative cooperativity CC within the dimer (PubMed:26063803). The same residues are used to bind CC DNA and ObgE (PubMed:36864742). {ECO:0000269|PubMed:26063803, CC ECO:0000269|PubMed:36864742}. CC -!- DISRUPTION PHENOTYPE: Deletion of the gene does not affect persistence CC significantly. {ECO:0000269|PubMed:36864742}. CC -!- SIMILARITY: Belongs to the anthranilate phosphoribosyltransferase CC family. TrpD2/YbiB subfamily. {ECO:0000305|PubMed:26063803}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; L02123; AAA53656.1; -; Genomic_DNA. DR EMBL; U00096; AAC73887.1; -; Genomic_DNA. DR EMBL; AP009048; BAA35466.1; -; Genomic_DNA. DR PIR; H64816; H64816. DR RefSeq; NP_415321.1; NC_000913.3. DR RefSeq; WP_000386551.1; NZ_CP009789.1. DR PDB; 4MUO; X-ray; 1.94 A; A/B=1-320. DR PDB; 8BFR; X-ray; 1.30 A; A=1-320. DR PDB; 8BFT; X-ray; 1.19 A; A=1-320. DR AlphaFoldDB; P30177; -. DR SASBDB; P30177; -. DR SMR; P30177; -. DR BioGRID; 4259965; 20. DR DIP; DIP-11425N; -. DR FunCoup; P30177; 104. DR IntAct; P30177; 14. DR STRING; 511145.b0800; -. DR jPOST; P30177; -. DR PaxDb; 511145-b0800; -. DR DNASU; 945424; -. DR EnsemblBacteria; AAC73887; AAC73887; b0800. DR GeneID; 75170865; -. DR GeneID; 75204915; -. DR GeneID; 945424; -. DR KEGG; ecj:JW0785; -. DR KEGG; eco:b0800; -. DR KEGG; ecoc:C3026_05050; -. DR PATRIC; fig|1411691.4.peg.1478; -. DR EchoBASE; EB1540; -. DR eggNOG; COG0547; Bacteria. DR HOGENOM; CLU_068658_0_0_6; -. DR InParanoid; P30177; -. DR OMA; AADLDWP; -. DR OrthoDB; 9768896at2; -. DR PhylomeDB; P30177; -. DR BioCyc; EcoCyc:EG11580-MONOMER; -. DR EvolutionaryTrace; P30177; -. DR PRO; PR:P30177; -. DR Proteomes; UP000000625; Chromosome. DR AbasyAtlas; P30177; -. DR GO; GO:0005829; C:cytosol; IDA:EcoCyc. DR GO; GO:0004048; F:anthranilate phosphoribosyltransferase activity; IEA:InterPro. DR GO; GO:0003677; F:DNA binding; IDA:EcoCyc. DR GO; GO:0042803; F:protein homodimerization activity; IDA:EcoCyc. DR GO; GO:0003723; F:RNA binding; IDA:EcoCyc. DR GO; GO:0000162; P:L-tryptophan biosynthetic process; IBA:GO_Central. DR FunFam; 1.20.970.10:FF:000005; Glycosyl transferase family protein; 1. DR FunFam; 3.40.1030.10:FF:000004; Glycosyl transferase family protein; 1. DR Gene3D; 3.40.1030.10; Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain; 1. DR Gene3D; 1.20.970.10; Transferase, Pyrimidine Nucleoside Phosphorylase, Chain C; 1. DR InterPro; IPR005940; Anthranilate_Pribosyl_Tfrase. DR InterPro; IPR017459; Glycosyl_Trfase_fam3_N_dom. DR InterPro; IPR036320; Glycosyl_Trfase_fam3_N_dom_sf. DR InterPro; IPR035902; Nuc_phospho_transferase. DR NCBIfam; NF006005; ybiB; 1. DR PANTHER; PTHR43285; ANTHRANILATE PHOSPHORIBOSYLTRANSFERASE; 1. DR PANTHER; PTHR43285:SF4; TRANSFERASE; 1. DR Pfam; PF02885; Glycos_trans_3N; 1. DR SUPFAM; SSF52418; Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain; 1. DR SUPFAM; SSF47648; Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain; 1. PE 1: Evidence at protein level; KW 3D-structure; Direct protein sequencing; DNA-binding; Reference proteome. FT CHAIN 1..320 FT /note="DNA-binding protein YbiB" FT /id="PRO_0000154530" FT MUTAGEN 40 FT /note="L->E: Forms monomers, but does not inhibit DNA FT binding and the monomeric variant shows an affinity FT comparable with that of the wild type; when associated with FT E-51." FT /evidence="ECO:0000269|PubMed:26063803" FT MUTAGEN 51 FT /note="I->E: Forms monomers, but does not inhibit DNA FT binding and the monomeric variant shows an affinity FT comparable with that of the wild type; when associated with FT E-40." FT /evidence="ECO:0000269|PubMed:26063803" FT MUTAGEN 92 FT /note="R->E: Loses binding to ObgE and shows a severe FT decrease in DNA binding." FT /evidence="ECO:0000269|PubMed:36864742" FT MUTAGEN 123 FT /note="R->E: Loses binding to ObgE and shows a severe FT decrease in DNA binding." FT /evidence="ECO:0000269|PubMed:36864742" FT HELIX 3..10 FT /evidence="ECO:0007829|PDB:8BFT" FT TURN 14..16 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 22..33 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 39..52 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 56..67 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 83..88 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 91..94 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 98..107 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 112..116 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 126..132 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 135..138 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 141..149 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 154..157 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 158..161 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 163..170 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 172..175 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 180..184 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 185..187 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 195..201 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 205..218 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 222..225 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 231..233 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 242..246 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 249..254 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 271..283 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 290..302 FT /evidence="ECO:0007829|PDB:8BFT" FT STRAND 305..308 FT /evidence="ECO:0007829|PDB:8BFT" FT HELIX 309..319 FT /evidence="ECO:0007829|PDB:8BFT" SQ SEQUENCE 320 AA; 35049 MW; 81B2A731E0C12390 CRC64; MDYRKIIKEI GRGKNHARDL DRDTARGLYA HMLNGEVPDL ELGGVLIALR IKGEGEAEML GFYEAMQNHT IKLTPPAGKP MPIVIPSYNG ARKQANLTPL LAILLHKLGF PVVVHGVSED PTRVLTETIF ELMGITPTLH GGQAQAKLDE HQPVFMPVGA FCPPLEKQLA MRWRMGVRNS AHTLAKLATP FAEGEALRLS SVSHPEYIGR VAKFFSDIGG RALLMHGTEG EVYANPQRCP QINLIDREGM RVLYEKQDTA GSELLPQAKD PETTAQWIER CLAGSEPIPE SLKIQMACCL VATGEAATIS DGLARVNQAF //