ROXA_ECOLI
ID ROXA_ECOLI Reviewed; 373 AA.
AC P27431; P75963;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=50S ribosomal protein L16 3-hydroxylase {ECO:0000305};
DE EC=1.14.11.47 {ECO:0000269|PubMed:23103944};
DE AltName: Full=Ribosomal oxygenase RoxA;
DE Short=ROX;
GN Name=roxA; Synonyms=ycfD; OrderedLocusNames=b1128, JW1114;
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 NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-280.
RC STRAIN=K12;
RX PubMed=1729240; DOI=10.1128/jb.174.2.492-498.1992;
RA Kasahara M., Nakata A., Shinagawa H.;
RT "Molecular analysis of the Escherichia coli phoP-phoQ operon.";
RL J. Bacteriol. 174:492-498(1992).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=23103944; DOI=10.1038/nchembio.1093;
RA Ge W., Wolf A., Feng T., Ho C.H., Sekirnik R., Zayer A., Granatino N.,
RA Cockman M.E., Loenarz C., Loik N.D., Hardy A.P., Claridge T.D., Hamed R.B.,
RA Chowdhury R., Gong L., Robinson C.V., Trudgian D.C., Jiang M.,
RA Mackeen M.M., McCullagh J.S., Gordiyenko Y., Thalhammer A., Yamamoto A.,
RA Yang M., Liu-Yi P., Zhang Z., Schmidt-Zachmann M., Kessler B.M.,
RA Ratcliffe P.J., Preston G.M., Coleman M.L., Schofield C.J.;
RT "Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and
RT humans.";
RL Nat. Chem. Biol. 8:960-962(2012).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH IRON, FUNCTION,
RP COFACTOR, SUBUNIT, AND MUTAGENESIS OF SER-116 AND ARG-140.
RC STRAIN=K12;
RX PubMed=24530688; DOI=10.1016/j.jmb.2014.02.008;
RA van Staalduinen L.M., Novakowski S.K., Jia Z.;
RT "Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe-
RT dependent oxygenase involved in translational regulation in Escherichia
RT coli.";
RL J. Mol. Biol. 426:1898-1910(2014).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEXES WITH 2-OXOGLUTARIC ACID
RP AND SUCCINATE, SUBUNIT, AND MUTAGENESIS OF ILE-211.
RX PubMed=24814345; DOI=10.1038/nature13263;
RA Chowdhury R., Sekirnik R., Brissett N.C., Krojer T., Ho C.H., Ng S.S.,
RA Clifton I.J., Ge W., Kershaw N.J., Fox G.C., Muniz J.R., Vollmar M.,
RA Phillips C., Pilka E.S., Kavanagh K.L., von Delft F., Oppermann U.,
RA McDonough M.A., Doherty A.J., Schofield C.J.;
RT "Ribosomal oxygenases are structurally conserved from prokaryotes to
RT humans.";
RL Nature 510:422-426(2014).
CC -!- FUNCTION: Growth-regulating oxygenase that catalyzes the hydroxylation
CC of 50S ribosomal protein L16 on 'Arg-81'. {ECO:0000269|PubMed:23103944,
CC ECO:0000269|PubMed:24530688}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + L-arginyl-[ribosomal protein uL16] + O2 =
CC (3R)-3-hydroxy-L-arginyl-[ribosomal protein uL16] + CO2 + succinate;
CC Xref=Rhea:RHEA:41556, Rhea:RHEA-COMP:10074, Rhea:RHEA-COMP:10075,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:29965, ChEBI:CHEBI:30031, ChEBI:CHEBI:78294;
CC EC=1.14.11.47; Evidence={ECO:0000269|PubMed:23103944};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:24530688};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000269|PubMed:24530688};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:24530688,
CC ECO:0000269|PubMed:24814345}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene grow similarly as wild-
CC type under standard conditions, but show reduced growth under low
CC nutrient conditions; this result correlates with a bulk protein
CC translation rate that is lower by a factor of three or four in the
CC deletion mutant strain than that in the wild-type. Deletion of this
CC gene also leads to loss of Rpl16 hydroxylation.
CC {ECO:0000269|PubMed:23103944}.
CC -!- SIMILARITY: Belongs to the ROX family. RoxA/YcfD subfamily.
CC {ECO:0000305}.
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DR EMBL; U00096; AAC74212.2; -; Genomic_DNA.
DR EMBL; AP009048; BAA35950.1; -; Genomic_DNA.
DR EMBL; D90393; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR PIR; E64857; E64857.
DR RefSeq; NP_415646.4; NC_000913.3.
DR RefSeq; WP_000456506.1; NZ_SSZK01000010.1.
DR PDB; 4CCL; X-ray; 2.60 A; A/B=1-373.
DR PDB; 4LIT; X-ray; 2.40 A; A=1-373.
DR PDB; 4LIU; X-ray; 2.70 A; A=2-373.
DR PDB; 4LIV; X-ray; 2.70 A; A=1-373.
DR PDB; 4NUB; X-ray; 2.70 A; A=1-373.
DR PDBsum; 4CCL; -.
DR PDBsum; 4LIT; -.
DR PDBsum; 4LIU; -.
DR PDBsum; 4LIV; -.
DR PDBsum; 4NUB; -.
DR AlphaFoldDB; P27431; -.
DR SMR; P27431; -.
DR BioGRID; 4260093; 11.
DR DIP; DIP-11535N; -.
DR IntAct; P27431; 13.
DR STRING; 511145.b1128; -.
DR jPOST; P27431; -.
DR PaxDb; P27431; -.
DR PRIDE; P27431; -.
DR EnsemblBacteria; AAC74212; AAC74212; b1128.
DR EnsemblBacteria; BAA35950; BAA35950; BAA35950.
DR GeneID; 945391; -.
DR KEGG; ecj:JW1114; -.
DR KEGG; eco:b1128; -.
DR PATRIC; fig|511145.12.peg.1175; -.
DR EchoBASE; EB1400; -.
DR eggNOG; COG2850; Bacteria.
DR HOGENOM; CLU_039125_0_0_6; -.
DR InParanoid; P27431; -.
DR OMA; VDQFVPE; -.
DR PhylomeDB; P27431; -.
DR BioCyc; EcoCyc:EG11430-MON; -.
DR BioCyc; MetaCyc:EG11430-MON; -.
DR BRENDA; 1.14.11.47; 2026.
DR PRO; PR:P27431; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0016706; F:2-oxoglutarate-dependent dioxygenase activity; IDA:EcoCyc.
DR GO; GO:0008198; F:ferrous iron binding; IDA:EcoCyc.
DR GO; GO:0030961; P:peptidyl-arginine hydroxylation; IMP:EcoCyc.
DR GO; GO:0043687; P:post-translational protein modification; IMP:EcoCyc.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR039994; JmjC_protein.
DR PANTHER; PTHR13096; PTHR13096; 1.
DR Pfam; PF08007; Cupin_4; 1.
DR SMART; SM00558; JmjC; 1.
DR PROSITE; PS51184; JMJC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Dioxygenase; Iron; Metal-binding; Oxidoreductase;
KW Reference proteome.
FT CHAIN 1..373
FT /note="50S ribosomal protein L16 3-hydroxylase"
FT /id="PRO_0000168830"
FT DOMAIN 92..219
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 114
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:24814345"
FT BINDING 125..127
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:24814345"
FT BINDING 125
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24530688"
FT BINDING 127
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24530688"
FT BINDING 140
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:24814345"
FT BINDING 187
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:24530688"
FT BINDING 187
FT /ligand="substrate"
FT /evidence="ECO:0000305|PubMed:24814345"
FT MUTAGEN 116
FT /note="S->A: Loss of binding of 2-oxoglutarate."
FT /evidence="ECO:0000269|PubMed:24530688"
FT MUTAGEN 140
FT /note="R->A: Loss of binding of 2-oxoglutarate."
FT /evidence="ECO:0000269|PubMed:24530688"
FT MUTAGEN 211
FT /note="I->R: Blocks dimerization. Loss of activity."
FT /evidence="ECO:0000269|PubMed:24814345"
FT HELIX 9..15
FT /evidence="ECO:0007829|PDB:4LIT"
FT TURN 16..19
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 22..24
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:4CCL"
FT HELIX 37..44
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 51..57
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 60..66
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 76..84
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 91..94
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 95..102
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 105..107
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 108..116
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 131..135
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 137..145
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 167..173
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 178..181
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 187..202
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 207..221
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 244..258
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 261..272
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 290..298
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 303..305
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 311..314
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 317..320
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 323..325
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 330..338
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 340..342
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 344..347
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 348..352
FT /evidence="ECO:0007829|PDB:4LIT"
FT HELIX 354..365
FT /evidence="ECO:0007829|PDB:4LIT"
FT STRAND 368..371
FT /evidence="ECO:0007829|PDB:4LIT"
SQ SEQUENCE 373 AA; 42579 MW; 5DC601513A578FD0 CRC64;
MEYQLTLNWP DFLERHWQKR PVVLKRGFNN FIDPISPDEL AGLAMESEVD SRLVSHQDGK
WQVSHGPFES YDHLGETNWS LLVQAVNHWH EPTAALMRPF RELPDWRIDD LMISFSVPGG
GVGPHLDQYD VFIIQGTGRR RWRVGEKLQM KQHCPHPDLL QVDPFEAIID EELEPGDILY
IPPGFPHEGY ALENAMNYSV GFRAPNTREL ISGFADYVLQ RELGGNYYSD PDVPPRAHPA
DVLPQEMDKL REMMLELINQ PEHFKQWFGE FISQSRHELD IAPPEPPYQP DEIYDALKQG
EVLVRLGGLR VLRIGDDVYA NGEKIDSPHR PALDALASNI ALTAENFGDA LEDPSFLAML
AALVNSGYWF FEG
