YGFZ_ECOLI
ID YGFZ_ECOLI Reviewed; 326 AA.
AC P0ADE8; P39179; Q2M9U3; Q46826;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=tRNA-modifying protein YgfZ;
GN Name=ygfZ; Synonyms=yzzW; OrderedLocusNames=b2898, JW2866;
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 / 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 [2]
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 [3]
RP PROTEIN SEQUENCE OF 2-13.
RC STRAIN=K12 / EMG2;
RX PubMed=9298646; DOI=10.1002/elps.1150180807;
RA Link A.J., Robison K., Church G.M.;
RT "Comparing the predicted and observed properties of proteins encoded in the
RT genome of Escherichia coli K-12.";
RL Electrophoresis 18:1259-1313(1997).
RN [4]
RP IDENTIFICATION BY MASS SPECTROMETRY.
RC STRAIN=B / BL21;
RX PubMed=10493123;
RX DOI=10.1002/(sici)1522-2683(19990801)20:11<2181::aid-elps2181>3.0.co;2-q;
RA Fountoulakis M., Takacs M.-F., Berndt P., Langen H., Takacs B.;
RT "Enrichment of low abundance proteins of Escherichia coli by hydroxyapatite
RT chromatography.";
RL Electrophoresis 20:2181-2195(1999).
RN [5]
RP FUNCTION.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=16359333; DOI=10.1111/j.1365-2958.2005.04932.x;
RA Ote T., Hashimoto M., Ikeuchi Y., Su'etsugu M., Suzuki T., Katayama T.,
RA Kato J.;
RT "Involvement of the Escherichia coli folate-binding protein YgfZ in RNA
RT modification and regulation of chromosomal replication initiation.";
RL Mol. Microbiol. 59:265-275(2006).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1-325, AND FOLATE BINDING.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=15489424; DOI=10.1128/jb.186.21.7134-7140.2004;
RA Teplyakov A., Obmolova G., Sarikaya E., Pullalarevu S., Krajewski W.,
RA Galkin A., Howard A.J., Herzberg O., Gilliland G.L.;
RT "Crystal structure of the YgfZ protein from Escherichia coli suggests a
RT folate-dependent regulatory role in one-carbon metabolism.";
RL J. Bacteriol. 186:7134-7140(2004).
CC -!- FUNCTION: Folate-binding protein involved in regulating the level of
CC ATP-DnaA and in the modification of some tRNAs. It is probably a key
CC factor in regulatory networks that act via tRNA modification, such as
CC initiation of chromosomal replication. {ECO:0000269|PubMed:16359333}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the tRNA-modifying YgfZ family. {ECO:0000305}.
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DR EMBL; U28375; AAA83079.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75936.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76963.1; -; Genomic_DNA.
DR PIR; B65074; B65074.
DR RefSeq; NP_417374.1; NC_000913.3.
DR RefSeq; WP_000886062.1; NZ_STEB01000001.1.
DR PDB; 1NRK; X-ray; 2.80 A; A=1-325.
DR PDB; 1VLY; X-ray; 1.30 A; A=1-326.
DR PDBsum; 1NRK; -.
DR PDBsum; 1VLY; -.
DR AlphaFoldDB; P0ADE8; -.
DR SMR; P0ADE8; -.
DR BioGRID; 4261457; 786.
DR DIP; DIP-48117N; -.
DR IntAct; P0ADE8; 6.
DR STRING; 511145.b2898; -.
DR SWISS-2DPAGE; P0ADE8; -.
DR jPOST; P0ADE8; -.
DR PaxDb; P0ADE8; -.
DR PRIDE; P0ADE8; -.
DR EnsemblBacteria; AAC75936; AAC75936; b2898.
DR EnsemblBacteria; BAE76963; BAE76963; BAE76963.
DR GeneID; 66673228; -.
DR GeneID; 947384; -.
DR KEGG; ecj:JW2866; -.
DR KEGG; eco:b2898; -.
DR PATRIC; fig|1411691.4.peg.3834; -.
DR EchoBASE; EB2549; -.
DR eggNOG; COG0354; Bacteria.
DR HOGENOM; CLU_007884_6_1_6; -.
DR InParanoid; P0ADE8; -.
DR OMA; VNFKKGC; -.
DR PhylomeDB; P0ADE8; -.
DR BioCyc; EcoCyc:G7511-MON; -.
DR EvolutionaryTrace; P0ADE8; -.
DR PRO; PR:P0ADE8; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005542; F:folic acid binding; IDA:EcoCyc.
DR GO; GO:0016226; P:iron-sulfur cluster assembly; IBA:GO_Central.
DR GO; GO:0009451; P:RNA modification; IEA:InterPro.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-UniRule.
DR HAMAP; MF_01175; tRNA_modifying_YgfZ; 1.
DR InterPro; IPR006222; GCV_T_N.
DR InterPro; IPR029043; GcvT/YgfZ_C.
DR InterPro; IPR023758; tRNA-modifying_YgfZ.
DR InterPro; IPR045179; YgfZ/GcvT.
DR InterPro; IPR017703; YgfZ/GcvT_CS.
DR PANTHER; PTHR22602; PTHR22602; 1.
DR Pfam; PF01571; GCV_T; 1.
DR SUPFAM; SSF101790; SSF101790; 1.
DR TIGRFAMs; TIGR03317; ygfZ_signature; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; Folate-binding;
KW Reference proteome; tRNA processing.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:9298646"
FT CHAIN 2..326
FT /note="tRNA-modifying protein YgfZ"
FT /id="PRO_0000169834"
FT BINDING 27
FT /ligand="folate"
FT /ligand_id="ChEBI:CHEBI:62501"
FT /evidence="ECO:0000255"
FT BINDING 189
FT /ligand="folate"
FT /ligand_id="ChEBI:CHEBI:62501"
FT /evidence="ECO:0000255"
FT CONFLICT 8
FT /note="P -> D (in Ref. 3; AA sequence)"
FT /evidence="ECO:0000305"
FT HELIX 14..16
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 19..23
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 27..34
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 37..42
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 45..47
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 49..51
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 57..63
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 69..78
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 81..87
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 88..99
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 103..106
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 114..122
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 125..130
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 139..141
FT /evidence="ECO:0007829|PDB:1NRK"
FT STRAND 143..146
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 149..154
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 156..158
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 160..165
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 167..177
FT /evidence="ECO:0007829|PDB:1VLY"
FT TURN 178..180
FT /evidence="ECO:0007829|PDB:1NRK"
FT STRAND 181..184
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 186..196
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 203..205
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 211..214
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 216..218
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 224..226
FT /evidence="ECO:0007829|PDB:1VLY"
FT HELIX 232..237
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 246..253
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 265..269
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 272..276
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 278..284
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 290..297
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 306..308
FT /evidence="ECO:0007829|PDB:1VLY"
FT STRAND 315..318
FT /evidence="ECO:0007829|PDB:1VLY"
SQ SEQUENCE 326 AA; 36094 MW; 08E050CE26B56B77 CRC64;
MAFTPFPPRQ PTASARLPLT LMTLDDWALA TITGADSEKY MQGQVTADVS QMAEDQHLLA
AHCDAKGKMW SNLRLFRDGD GFAWIERRSV REPQLTELKK YAVFSKVTIA PDDERVLLGV
AGFQARAALA NLFSELPSKE KQVVKEGATT LLWFEHPAER FLIVTDEATA NMLTDKLRGE
AELNNSQQWL ALNIEAGFPV IDAANSGQFI PQATNLQALG GISFKKGCYT GQEMVARAKF
RGANKRALWL LAGSASRLPE AGEDLELKMG ENWRRTGTVL AAVKLEDGQV VVQVVMNNDM
EPDSIFRVRD DANTLHIEPL PYSLEE
