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Protein

50S ribosomal protein L16 3-hydroxylase

Gene

roxA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Growth-regulating oxygenase that catalyzes the hydroxylation of 50S ribosomal protein L16 on 'Arg-81'.2 Publications

Catalytic activityi

[50S ribosomal protein L16]-L-Arg(81) + 2-oxoglutarate + O2 = [50S ribosomal protein L16]-(3R)-3-hydroxy-L-Arg(81) + succinate + CO2.1 Publication

Cofactori

Fe2+1 PublicationNote: Binds 1 Fe2+ ion per subunit.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei114 – 1141Substrate1 Publication
Metal bindingi125 – 1251Iron; via tele nitrogen; catalytic1 Publication
Metal bindingi127 – 1271Iron; catalytic1 Publication
Binding sitei140 – 1401Substrate1 Publication
Metal bindingi187 – 1871Iron; via tele nitrogen; catalytic1 Publication
Binding sitei187 – 1871Substrate1 Publication

GO - Molecular functioni

GO - Biological processi

  • peptidyl-arginine hydroxylation Source: EcoCyc
  • post-translational protein modification Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11430-MONOMER.
ECOL316407:JW1114-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
50S ribosomal protein L16 3-hydroxylaseCurated (EC:1.14.11.471 Publication)
Alternative name(s):
Ribosomal oxygenase RoxA
Short name:
ROX
Gene namesi
Name:roxAImported
Synonyms:ycfD
Ordered Locus Names:b1128, JW1114
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11430. roxA.

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene grow similarly as wild-type under standard conditions, but show reduced growth under low nutrient conditions; this result correlates with a bulk protein translation rate that is lower by a factor of three or four in the deletion mutant strain than that in the wild-type. Deletion of this gene also leads to loss of Rpl16 hydroxylation.1 Publication

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi116 – 1161S → A: Loss of binding of 2-oxoglutarate. 1 Publication
Mutagenesisi140 – 1401R → A: Loss of binding of 2-oxoglutarate. 1 Publication
Mutagenesisi211 – 2111I → R: Blocks dimerization. Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 37337350S ribosomal protein L16 3-hydroxylasePRO_0000168830Add
BLAST

Proteomic databases

EPDiP27431.
PaxDbiP27431.
PRIDEiP27431.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

BioGridi4260093. 7 interactions.
DIPiDIP-11535N.
IntActiP27431. 12 interactions.
STRINGi511145.b1128.

Structurei

Secondary structure

1
373
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi9 – 157Combined sources
Turni16 – 194Combined sources
Beta strandi22 – 243Combined sources
Beta strandi27 – 304Combined sources
Helixi37 – 448Combined sources
Beta strandi51 – 577Combined sources
Beta strandi60 – 667Combined sources
Beta strandi76 – 849Combined sources
Helixi86 – 883Combined sources
Helixi91 – 944Combined sources
Helixi95 – 1028Combined sources
Helixi105 – 1073Combined sources
Beta strandi108 – 1169Combined sources
Beta strandi131 – 1355Combined sources
Beta strandi137 – 1459Combined sources
Beta strandi167 – 1737Combined sources
Beta strandi178 – 1814Combined sources
Beta strandi187 – 20216Combined sources
Helixi207 – 22115Combined sources
Helixi244 – 25815Combined sources
Helixi261 – 27212Combined sources
Helixi290 – 2989Combined sources
Beta strandi303 – 3053Combined sources
Beta strandi311 – 3144Combined sources
Beta strandi317 – 3204Combined sources
Beta strandi323 – 3253Combined sources
Helixi330 – 3389Combined sources
Beta strandi340 – 3423Combined sources
Helixi344 – 3474Combined sources
Helixi348 – 3525Combined sources
Helixi354 – 36512Combined sources
Beta strandi368 – 3714Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4CCLX-ray2.60A/B1-373[»]
4LITX-ray2.40A1-373[»]
4LIUX-ray2.70A2-373[»]
4LIVX-ray2.70A1-373[»]
4NUBX-ray2.70A1-373[»]
ProteinModelPortaliP27431.
SMRiP27431. Positions 1-372.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini92 – 219128JmjCPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni125 – 1273Substrate-binding1 Publication

Sequence similaritiesi

Belongs to the ROX family. RoxA/YcfD subfamily.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG4105EZE. Bacteria.
COG2850. LUCA.
HOGENOMiHOG000261963.
InParanoidiP27431.
KOiK18850.
OMAiFTPIIDV.
OrthoDBiEOG683S5N.
PhylomeDBiP27431.

Family and domain databases

InterProiIPR003347. JmjC_dom.
[Graphical view]
PfamiPF08007. Cupin_4. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P27431-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEYQLTLNWP DFLERHWQKR PVVLKRGFNN FIDPISPDEL AGLAMESEVD
60 70 80 90 100
SRLVSHQDGK WQVSHGPFES YDHLGETNWS LLVQAVNHWH EPTAALMRPF
110 120 130 140 150
RELPDWRIDD LMISFSVPGG GVGPHLDQYD VFIIQGTGRR RWRVGEKLQM
160 170 180 190 200
KQHCPHPDLL QVDPFEAIID EELEPGDILY IPPGFPHEGY ALENAMNYSV
210 220 230 240 250
GFRAPNTREL ISGFADYVLQ RELGGNYYSD PDVPPRAHPA DVLPQEMDKL
260 270 280 290 300
REMMLELINQ PEHFKQWFGE FISQSRHELD IAPPEPPYQP DEIYDALKQG
310 320 330 340 350
EVLVRLGGLR VLRIGDDVYA NGEKIDSPHR PALDALASNI ALTAENFGDA
360 370
LEDPSFLAML AALVNSGYWF FEG
Length:373
Mass (Da):42,579
Last modified:November 1, 1997 - v2
Checksum:i5DC601513A578FD0
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74212.2.
AP009048 Genomic DNA. Translation: BAA35950.1.
D90393 Genomic DNA. No translation available.
PIRiE64857.
RefSeqiNP_415646.4. NC_000913.3.
WP_000456506.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC74212; AAC74212; b1128.
BAA35950; BAA35950; BAA35950.
GeneIDi945391.
KEGGiecj:JW1114.
eco:b1128.
PATRICi32117505. VBIEscCol129921_1175.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74212.2.
AP009048 Genomic DNA. Translation: BAA35950.1.
D90393 Genomic DNA. No translation available.
PIRiE64857.
RefSeqiNP_415646.4. NC_000913.3.
WP_000456506.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4CCLX-ray2.60A/B1-373[»]
4LITX-ray2.40A1-373[»]
4LIUX-ray2.70A2-373[»]
4LIVX-ray2.70A1-373[»]
4NUBX-ray2.70A1-373[»]
ProteinModelPortaliP27431.
SMRiP27431. Positions 1-372.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260093. 7 interactions.
DIPiDIP-11535N.
IntActiP27431. 12 interactions.
STRINGi511145.b1128.

Proteomic databases

EPDiP27431.
PaxDbiP27431.
PRIDEiP27431.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74212; AAC74212; b1128.
BAA35950; BAA35950; BAA35950.
GeneIDi945391.
KEGGiecj:JW1114.
eco:b1128.
PATRICi32117505. VBIEscCol129921_1175.

Organism-specific databases

EchoBASEiEB1400.
EcoGeneiEG11430. roxA.

Phylogenomic databases

eggNOGiENOG4105EZE. Bacteria.
COG2850. LUCA.
HOGENOMiHOG000261963.
InParanoidiP27431.
KOiK18850.
OMAiFTPIIDV.
OrthoDBiEOG683S5N.
PhylomeDBiP27431.

Enzyme and pathway databases

BioCyciEcoCyc:EG11430-MONOMER.
ECOL316407:JW1114-MONOMER.

Miscellaneous databases

PROiP27431.

Family and domain databases

InterProiIPR003347. JmjC_dom.
[Graphical view]
PfamiPF08007. Cupin_4. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Molecular analysis of the Escherichia coli phoP-phoQ operon."
    Kasahara M., Nakata A., Shinagawa H.
    J. Bacteriol. 174:492-498(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-280.
    Strain: K12.
  5. Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE.
    Strain: K12.
  6. "Structure and functional analysis of YcfD, a novel 2-oxoglutarate/Fe-dependent oxygenase involved in translational regulation in Escherichia coli."
    van Staalduinen L.M., Novakowski S.K., Jia Z.
    J. Mol. Biol. 426:1898-1910(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH IRON, FUNCTION, COFACTOR, SUBUNIT, MUTAGENESIS OF SER-116 AND ARG-140.
    Strain: K12.
  7. Cited for: X-RAY CRYSTALLOGRAPHY (2.40 ANGSTROMS) IN COMPLEXES WITH 2-OXOGLUTARIC ACID AND SUCCINATE, SUBUNIT, MUTAGENESIS OF ILE-211.

Entry informationi

Entry nameiROXA_ECOLI
AccessioniPrimary (citable) accession number: P27431
Secondary accession number(s): P75963
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: November 1, 1997
Last modified: March 16, 2016
This is version 111 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.