YBCO_ECOLI
ID YBCO_ECOLI Reviewed; 96 AA.
AC P68661; Q2MBN2; Q37872; Q47271;
DT 07-DEC-2004, integrated into UniProtKB/Swiss-Prot.
DT 07-DEC-2004, sequence version 1.
DT 03-AUG-2022, entry version 95.
DE RecName: Full=Putative nuclease YbcO;
DE EC=3.1.-.-;
GN Name=ybcO; OrderedLocusNames=b0549, JW0537;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8648624; DOI=10.1006/jmbi.1996.0185;
RA Mahdi A.A., Sharples G.J., Mandal T.N., Lloyd R.G.;
RT "Holliday junction resolvases encoded by homologous rusA genes in
RT Escherichia coli K-12 and phage 82.";
RL J. Mol. Biol. 257:561-573(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RA Chung E., Allen E., Araujo R., Aparicio A.M., Davis K., Duncan M.,
RA Federspiel N., Hyman R., Kalman S., Komp C., Kurdi O., Lew H., Lin D.,
RA Namath A., Oefner P., Roberts D., Schramm S., Davis R.W.;
RT "Sequence of minutes 4-25 of Escherichia coli.";
RL Submitted (JAN-1997) to the EMBL/GenBank/DDBJ databases.
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 PREDICTION OF FUNCTION, AND ACTIVE SITE PREDICTION.
RX PubMed=27562564; DOI=10.1038/srep32070;
RA Kaur G., Subramanian S.;
RT "Classification of the treble clef zinc finger: noteworthy lessons for
RT structure and function evolution.";
RL Sci. Rep. 6:32070-32070(2016).
RN [6] {ECO:0007744|PDB:3G27}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) IN COMPLEX WITH ZINC.
RA Cuff M.E., Evdokimova E., Kudritska M., Edwards A., Savchenko A.,
RA Joachimiak A.;
RT "Structure of a putative bacteriophage protein from Escherichia coli str.
RT K-12 substr. MG1655.";
RL Submitted (JAN-2009) to the PDB data bank.
CC -!- FUNCTION: Based on its fold and a conserved His residue, has been
CC predicted to be a nuclease. {ECO:0000305|PubMed:27562564}.
CC -!- MISCELLANEOUS: Encoded by the cryptic lambdoid prophage DLP12.
CC -!- SIMILARITY: Belongs to the YbcO family. {ECO:0000305}.
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DR EMBL; X92587; CAA63320.1; -; Genomic_DNA.
DR EMBL; U82598; AAB40745.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73650.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76324.1; -; Genomic_DNA.
DR PIR; C64787; C64787.
DR RefSeq; NP_415081.1; NC_000913.3.
DR RefSeq; WP_000774486.1; NZ_LN832404.1.
DR PDB; 3G27; X-ray; 2.10 A; A=1-96.
DR PDBsum; 3G27; -.
DR AlphaFoldDB; P68661; -.
DR SMR; P68661; -.
DR BioGRID; 4261524; 160.
DR IntAct; P68661; 1.
DR STRING; 511145.b0549; -.
DR PaxDb; P68661; -.
DR PRIDE; P68661; -.
DR DNASU; 945147; -.
DR EnsemblBacteria; AAC73650; AAC73650; b0549.
DR EnsemblBacteria; BAE76324; BAE76324; BAE76324.
DR GeneID; 945147; -.
DR KEGG; ecj:JW0537; -.
DR KEGG; eco:b0549; -.
DR PATRIC; fig|511145.12.peg.570; -.
DR EchoBASE; EB3396; -.
DR eggNOG; ENOG5032TP3; Bacteria.
DR HOGENOM; CLU_155134_1_0_6; -.
DR OMA; PGICNGD; -.
DR PhylomeDB; P68661; -.
DR BioCyc; EcoCyc:G6305-MON; -.
DR EvolutionaryTrace; P68661; -.
DR PRO; PR:P68661; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004518; F:nuclease activity; IEA:UniProtKB-KW.
DR InterPro; IPR010774; YbcO.
DR Pfam; PF07102; DUF1364; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Nuclease; Reference proteome; Zinc.
FT CHAIN 1..96
FT /note="Putative nuclease YbcO"
FT /id="PRO_0000168654"
FT ACT_SITE 32
FT /note="Proton acceptor"
FT /evidence="ECO:0000305|PubMed:27562564"
FT BINDING 13
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0007744|PDB:3G27"
FT BINDING 21
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0007744|PDB:3G27"
FT BINDING 54
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0007744|PDB:3G27"
FT BINDING 57
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0007744|PDB:3G27"
FT TURN 7..10
FT /evidence="ECO:0007829|PDB:3G27"
FT TURN 18..20
FT /evidence="ECO:0007829|PDB:3G27"
FT HELIX 25..27
FT /evidence="ECO:0007829|PDB:3G27"
FT STRAND 29..32
FT /evidence="ECO:0007829|PDB:3G27"
FT STRAND 47..53
FT /evidence="ECO:0007829|PDB:3G27"
FT HELIX 55..61
FT /evidence="ECO:0007829|PDB:3G27"
FT HELIX 70..90
FT /evidence="ECO:0007829|PDB:3G27"
SQ SEQUENCE 96 AA; 10348 MW; AB066A8AE7B273C7 CRC64;
MADLRKAARG RECQVRIPGV CNGNPETSVL AHIRLTGLCG TGTKPPDLIA TIACSACHDE
IDRRTHFVDA GYAKECALEG MARTQVIWLK EGVIKA
