YCDX_ECOLI
ID YCDX_ECOLI Reviewed; 245 AA.
AC P75914;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 155.
DE RecName: Full=Probable phosphatase YcdX {ECO:0000255|HAMAP-Rule:MF_01561};
DE EC=3.1.3.- {ECO:0000255|HAMAP-Rule:MF_01561};
GN Name=ycdX {ECO:0000255|HAMAP-Rule:MF_01561};
GN OrderedLocusNames=b1034, JW1017;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
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 [2]
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 [3]
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 [4]
RP FUNCTION, ACTIVITY REGULATION, INTERACTION WITH YCDY, DISRUPTION PHENOTYPE,
RP AND IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=K12 / BW25113;
RX PubMed=21965574; DOI=10.1128/jb.05927-11;
RA Redelberger D., Seduk F., Genest O., Mejean V., Leimkuhler S.,
RA Iobbi-Nivol C.;
RT "YcdY protein of Escherichia coli, an atypical member of the TorD chaperone
RT family.";
RL J. Bacteriol. 193:6512-6516(2011).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.57 ANGSTROMS) IN COMPLEX WITH ZINC IONS, COFACTOR,
RP AND SUBUNIT.
RX PubMed=12661000; DOI=10.1002/prot.10352;
RA Teplyakov A., Obmolova G., Khil P.P., Howard A.J., Camerini-Otero R.D.,
RA Gilliland G.L.;
RT "Crystal structure of the Escherichia coli YcdX protein reveals a
RT trinuclear zinc active site.";
RL Proteins 51:315-318(2003).
CC -!- FUNCTION: Hydrolyzes p-nitrophenyl phosphate (pNPP) in vitro. Involved
CC in the swarming motility process. {ECO:0000269|PubMed:21965574}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12661000};
CC Note=Binds 3 Zn(2+) ions per subunit. {ECO:0000269|PubMed:12661000};
CC -!- ACTIVITY REGULATION: Activity is stimulated by YcdY.
CC {ECO:0000269|PubMed:21965574}.
CC -!- SUBUNIT: Homotrimer. Interacts with YcdY. {ECO:0000255|HAMAP-
CC Rule:MF_01561, ECO:0000269|PubMed:12661000,
CC ECO:0000269|PubMed:21965574}.
CC -!- INTERACTION:
CC P75914; P75915: ycdY; NbExp=2; IntAct=EBI-1121626, EBI-1121634;
CC -!- DISRUPTION PHENOTYPE: Mutants show no swarming ability.
CC {ECO:0000269|PubMed:21965574}.
CC -!- SIMILARITY: Belongs to the PHP family. {ECO:0000255|HAMAP-
CC Rule:MF_01561}.
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DR EMBL; U00096; AAC74118.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35815.1; -; Genomic_DNA.
DR PIR; G64845; G64845.
DR RefSeq; NP_415552.1; NC_000913.3.
DR RefSeq; WP_000283667.1; NZ_SSZK01000090.1.
DR PDB; 1M65; X-ray; 1.57 A; A=1-245.
DR PDB; 1M68; X-ray; 2.30 A; A=1-245.
DR PDB; 1PB0; X-ray; 1.95 A; A/B/C=1-245.
DR PDBsum; 1M65; -.
DR PDBsum; 1M68; -.
DR PDBsum; 1PB0; -.
DR AlphaFoldDB; P75914; -.
DR SMR; P75914; -.
DR BioGRID; 4260061; 149.
DR IntAct; P75914; 8.
DR STRING; 511145.b1034; -.
DR DrugBank; DB01942; Formic acid.
DR jPOST; P75914; -.
DR PaxDb; P75914; -.
DR PRIDE; P75914; -.
DR EnsemblBacteria; AAC74118; AAC74118; b1034.
DR EnsemblBacteria; BAA35815; BAA35815; BAA35815.
DR GeneID; 948477; -.
DR KEGG; ecj:JW1017; -.
DR KEGG; eco:b1034; -.
DR PATRIC; fig|1411691.4.peg.1237; -.
DR EchoBASE; EB3629; -.
DR eggNOG; COG1387; Bacteria.
DR HOGENOM; CLU_061999_0_1_6; -.
DR InParanoid; P75914; -.
DR OMA; SEPNCRA; -.
DR PhylomeDB; P75914; -.
DR BioCyc; EcoCyc:G6540-MON; -.
DR EvolutionaryTrace; P75914; -.
DR PRO; PR:P75914; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0016791; F:phosphatase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042578; F:phosphoric ester hydrolase activity; IDA:EcoCyc.
DR GO; GO:0008270; F:zinc ion binding; IDA:EcoCyc.
DR GO; GO:0071978; P:bacterial-type flagellum-dependent swarming motility; IMP:EcoCyc.
DR HAMAP; MF_01561; YcdX_phosphat; 1.
DR InterPro; IPR023710; Phosphatase_YcdX_put.
DR InterPro; IPR004013; PHP_dom.
DR InterPro; IPR003141; Pol/His_phosphatase_N.
DR InterPro; IPR016195; Pol/histidinol_Pase-like.
DR Pfam; PF02811; PHP; 1.
DR SMART; SM00481; POLIIIAc; 1.
DR SUPFAM; SSF89550; SSF89550; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..245
FT /note="Probable phosphatase YcdX"
FT /id="PRO_0000013818"
FT BINDING 7
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 9
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 15
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 40
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 73
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 73
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 101
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 131
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="3"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 192
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:12661000"
FT BINDING 194
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:12661000"
FT HELIX 20..30
FT /evidence="ECO:0007829|PDB:1M65"
FT STRAND 34..40
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 51..54
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 55..58
FT /evidence="ECO:0007829|PDB:1M65"
FT STRAND 61..63
FT /evidence="ECO:0007829|PDB:1M65"
FT STRAND 66..76
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 87..92
FT /evidence="ECO:0007829|PDB:1M65"
FT STRAND 94..99
FT /evidence="ECO:0007829|PDB:1M65"
FT TURN 102..104
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 110..122
FT /evidence="ECO:0007829|PDB:1M65"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 141..151
FT /evidence="ECO:0007829|PDB:1M65"
FT STRAND 154..158
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 173..183
FT /evidence="ECO:0007829|PDB:1M65"
FT STRAND 187..190
FT /evidence="ECO:0007829|PDB:1M65"
FT STRAND 193..195
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 203..211
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 216..218
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 224..233
FT /evidence="ECO:0007829|PDB:1M65"
FT HELIX 240..242
FT /evidence="ECO:0007829|PDB:1M65"
SQ SEQUENCE 245 AA; 26891 MW; 19ADC0EF462D49D3 CRC64;
MYPVDLHMHT VASTHAYSTL SDYIAQAKQK GIKLFAITDH GPDMEDAPHH WHFINMRIWP
RVVDGVGILR GIEANIKNVD GEIDCSGKMF DSLDLIIAGF HEPVFAPHDK ATNTQAMIAT
IASGNVHIIS HPGNPKYEID VKAVAEAAAK HQVALEINNS SFLHSRKGSE DNCREVAAAV
RDAGGWVALG SDSHTAFTMG EFEECLKILD AVDFPPERIL NVSPRRLLNF LESRGMAPIA
EFADL
