RAPZ_ECOLI
ID RAPZ_ECOLI Reviewed; 284 AA.
AC P0A894; P33995; Q2M907;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-JUN-2005, sequence version 1.
DT 03-AUG-2022, entry version 127.
DE RecName: Full=RNase adapter protein RapZ {ECO:0000255|HAMAP-Rule:MF_00636, ECO:0000303|PubMed:23475961};
GN Name=rapZ {ECO:0000255|HAMAP-Rule:MF_00636, ECO:0000303|PubMed:23475961};
GN Synonyms=yhbJ; OrderedLocusNames=b3205, JW3172;
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;
RX PubMed=8025669; DOI=10.1099/13500872-140-5-1035;
RA Jones D.H.A., Franklin C.F.H., Thomas C.M.;
RT "Molecular analysis of the operon which encodes the RNA polymerase sigma
RT factor sigma 54 of Escherichia coli.";
RL Microbiology 140:1035-1043(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=7876255; DOI=10.1074/jbc.270.9.4822;
RA Powell B.S., Court D.L., Inada T., Nakamura Y., Michotey V., Cui X.,
RA Reizer A., Saier M.H. Jr., Reizer J.;
RT "Novel proteins of the phosphotransferase system encoded within the rpoN
RT operon of Escherichia coli. Enzyme IIANtr affects growth on organic
RT nitrogen and the conditional lethality of an erats mutant.";
RL J. Biol. Chem. 270:4822-4839(1995).
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 FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=17824929; DOI=10.1111/j.1365-2958.2007.05888.x;
RA Kalamorz F., Reichenbach B., Maerz W., Rak B., Goerke B.;
RT "Feedback control of glucosamine-6-phosphate synthase GlmS expression
RT depends on the small RNA GlmZ and involves the novel protein YhbJ in
RT Escherichia coli.";
RL Mol. Microbiol. 65:1518-1533(2007).
RN [6]
RP FUNCTION, AND NTPASE ACTIVITY.
RX PubMed=19074378; DOI=10.1128/jb.01493-08;
RA Luciano J., Foulquier E., Fantino J.R., Galinier A., Pompeo F.;
RT "Characterization of YvcJ, a conserved P-loop-containing protein, and its
RT implication in competence in Bacillus subtilis.";
RL J. Bacteriol. 191:1556-1564(2009).
RN [7]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-251, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=K12 / JW1106, and K12 / MG1655 / ATCC 47076;
RX PubMed=18723842; DOI=10.1074/mcp.m800187-mcp200;
RA Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.F.,
RA Grishin N.V., Zhao Y.;
RT "Lysine acetylation is a highly abundant and evolutionarily conserved
RT modification in Escherichia coli.";
RL Mol. Cell. Proteomics 8:215-225(2009).
RN [8]
RP FUNCTION, INTERACTION WITH GLMY; GLMZ AND RNASE E, RNA-BINDING, AND
RP MUTAGENESIS OF LYS-270; LYS-281; ARG-282 AND LYS-283.
RX PubMed=23475961; DOI=10.1101/gad.210112.112;
RA Gopel Y., Papenfort K., Reichenbach B., Vogel J., Gorke B.;
RT "Targeted decay of a regulatory small RNA by an adaptor protein for RNase E
RT and counteraction by an anti-adaptor RNA.";
RL Genes Dev. 27:552-564(2013).
RN [9]
RP CRYSTALLIZATION, AND SUBUNIT.
RX PubMed=23385747; DOI=10.1107/s1744309112048622;
RA Resch M., Gopel Y., Gorke B., Ficner R.;
RT "Crystallization and preliminary X-ray diffraction analysis of YhbJ from
RT Escherichia coli, a key protein involved in the GlmYZ sRNA regulatory
RT cascade.";
RL Acta Crystallogr. F 69:109-114(2013).
CC -!- FUNCTION: Modulates the synthesis of GlmS, by affecting the processing
CC and stability of the regulatory small RNA GlmZ. When glucosamine-6-
CC phosphate (GlcN6P) concentrations are high in the cell, RapZ binds GlmZ
CC and targets it to cleavage by RNase E. Consequently, GlmZ is
CC inactivated and unable to activate GlmS synthesis. Under low GlcN6P
CC concentrations, RapZ is sequestered and inactivated by an other
CC regulatory small RNA, GlmY, preventing GlmZ degradation and leading to
CC synthesis of GlmS (PubMed:17824929, PubMed:23475961). Displays ATPase
CC and GTPase activities in vitro. Can also hydrolyze pNPP
CC (PubMed:19074378). {ECO:0000269|PubMed:17824929,
CC ECO:0000269|PubMed:19074378, ECO:0000269|PubMed:23475961}.
CC -!- SUBUNIT: Homotrimer (PubMed:23385747). Interacts with the small RNAs
CC GlmY and GlmZ (PubMed:23475961). Interacts with the catalytic domain of
CC RNase E in an RNA-independent manner (PubMed:23475961).
CC {ECO:0000269|PubMed:23385747, ECO:0000269|PubMed:23475961}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene strongly overproduce the
CC GlmS protein. {ECO:0000269|PubMed:17824929}.
CC -!- SIMILARITY: Belongs to the RapZ-like family. RapZ subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00636, ECO:0000305}.
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DR EMBL; Z27094; CAA81620.1; -; Genomic_DNA.
DR EMBL; U12684; AAB60166.1; -; Genomic_DNA.
DR EMBL; U18997; AAA58007.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76237.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77249.1; -; Genomic_DNA.
DR PIR; I76721; I76721.
DR RefSeq; NP_417672.1; NC_000913.3.
DR RefSeq; WP_000243741.1; NZ_STEB01000012.1.
DR PDB; 5O5O; X-ray; 3.40 A; A/B/C/D=1-284.
DR PDB; 5O5Q; X-ray; 3.25 A; A/B/C/D=1-284.
DR PDB; 5O5S; X-ray; 1.17 A; A=154-284.
DR PDBsum; 5O5O; -.
DR PDBsum; 5O5Q; -.
DR PDBsum; 5O5S; -.
DR AlphaFoldDB; P0A894; -.
DR SMR; P0A894; -.
DR BioGRID; 4259285; 32.
DR DIP; DIP-35927N; -.
DR IntAct; P0A894; 15.
DR STRING; 511145.b3205; -.
DR iPTMnet; P0A894; -.
DR jPOST; P0A894; -.
DR PaxDb; P0A894; -.
DR PRIDE; P0A894; -.
DR EnsemblBacteria; AAC76237; AAC76237; b3205.
DR EnsemblBacteria; BAE77249; BAE77249; BAE77249.
DR GeneID; 67415961; -.
DR GeneID; 947727; -.
DR KEGG; ecj:JW3172; -.
DR KEGG; eco:b3205; -.
DR PATRIC; fig|1411691.4.peg.3526; -.
DR EchoBASE; EB2066; -.
DR eggNOG; COG1660; Bacteria.
DR HOGENOM; CLU_059558_1_1_6; -.
DR InParanoid; P0A894; -.
DR OMA; TVMSFGF; -.
DR PhylomeDB; P0A894; -.
DR BioCyc; EcoCyc:EG12146-MON; -.
DR PRO; PR:P0A894; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0032991; C:protein-containing complex; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0097367; F:carbohydrate derivative binding; IDA:EcoCyc.
DR GO; GO:0005525; F:GTP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0060090; F:molecular adaptor activity; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IDA:EcoCyc.
DR GO; GO:0050779; P:RNA destabilization; IMP:EcoCyc.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00636; RapZ_like; 1.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR005337; RapZ-like.
DR PANTHER; PTHR30448; PTHR30448; 1.
DR Pfam; PF03668; ATP_bind_2; 1.
DR PIRSF; PIRSF005052; P-loopkin; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; ATP-binding; GTP-binding; Nucleotide-binding;
KW Reference proteome; RNA-binding.
FT CHAIN 1..284
FT /note="RNase adapter protein RapZ"
FT /id="PRO_0000107705"
FT REGION 266..284
FT /note="RNA-binding"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00636,
FT ECO:0000305|PubMed:23475961"
FT BINDING 8..15
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00636"
FT BINDING 56..59
FT /ligand="GTP"
FT /ligand_id="ChEBI:CHEBI:37565"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00636"
FT MOD_RES 251
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000269|PubMed:18723842"
FT MUTAGEN 270
FT /note="K->A: Lack of activity. Does not bind GlmY and GlmZ;
FT when associated with A-281; A-282 and A-283."
FT /evidence="ECO:0000269|PubMed:23475961"
FT MUTAGEN 281
FT /note="K->A: Lack of activity. Does not bind GlmY and GlmZ;
FT when associated with A-270; A-282 and A-283."
FT /evidence="ECO:0000269|PubMed:23475961"
FT MUTAGEN 282
FT /note="R->A: Lack of activity. Does not bind GlmY and GlmZ;
FT when associated with A-270; A-281 and A-283."
FT /evidence="ECO:0000269|PubMed:23475961"
FT MUTAGEN 283
FT /note="K->A: Lack of activity. Does not bind GlmY and GlmZ;
FT when associated with A-270; A-281 and A-282."
FT /evidence="ECO:0000269|PubMed:23475961"
FT STRAND 1..9
FT /evidence="ECO:0007829|PDB:5O5Q"
FT HELIX 14..24
FT /evidence="ECO:0007829|PDB:5O5Q"
FT STRAND 27..31
FT /evidence="ECO:0007829|PDB:5O5Q"
FT HELIX 34..36
FT /evidence="ECO:0007829|PDB:5O5Q"
FT HELIX 37..45
FT /evidence="ECO:0007829|PDB:5O5Q"
FT TURN 46..48
FT /evidence="ECO:0007829|PDB:5O5Q"
FT STRAND 51..55
FT /evidence="ECO:0007829|PDB:5O5Q"
FT TURN 57..59
FT /evidence="ECO:0007829|PDB:5O5Q"
FT HELIX 64..72
FT /evidence="ECO:0007829|PDB:5O5Q"
FT STRAND 78..86
FT /evidence="ECO:0007829|PDB:5O5Q"
FT HELIX 89..96
FT /evidence="ECO:0007829|PDB:5O5Q"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:5O5Q"
FT HELIX 113..122
FT /evidence="ECO:0007829|PDB:5O5Q"
FT HELIX 124..128
FT /evidence="ECO:0007829|PDB:5O5Q"
FT STRAND 131..135
FT /evidence="ECO:0007829|PDB:5O5Q"
FT HELIX 141..151
FT /evidence="ECO:0007829|PDB:5O5Q"
FT STRAND 161..168
FT /evidence="ECO:0007829|PDB:5O5S"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:5O5S"
FT STRAND 178..182
FT /evidence="ECO:0007829|PDB:5O5S"
FT HELIX 189..191
FT /evidence="ECO:0007829|PDB:5O5S"
FT TURN 193..197
FT /evidence="ECO:0007829|PDB:5O5S"
FT HELIX 203..210
FT /evidence="ECO:0007829|PDB:5O5S"
FT HELIX 213..233
FT /evidence="ECO:0007829|PDB:5O5S"
FT STRAND 239..252
FT /evidence="ECO:0007829|PDB:5O5S"
FT HELIX 253..267
FT /evidence="ECO:0007829|PDB:5O5S"
FT STRAND 271..276
FT /evidence="ECO:0007829|PDB:5O5S"
FT TURN 277..280
FT /evidence="ECO:0007829|PDB:5O5S"
SQ SEQUENCE 284 AA; 32492 MW; BB1525B1E044126C CRC64;
MVLMIVSGRS GSGKSVALRA LEDMGFYCVD NLPVVLLPDL ARTLADREIS AAVSIDVRNM
PESPEIFEQA MSNLPDAFSP QLLFLDADRN TLIRRYSDTR RLHPLSSKNL SLESAIDKES
DLLEPLRSRA DLIVDTSEMS VHELAEMLRT RLLGKREREL TMVFESFGFK HGIPIDADYV
FDVRFLPNPH WDPKLRPMTG LDKPVAAFLD RHTEVHNFIY QTRSYLELWL PMLETNNRSY
LTVAIGCTGG KHRSVYIAEQ LADYFRSRGK NVQSRHRTLE KRKP
