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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)DescriptionActionsGraphical viewLength
Binding sitei114Substrate1 Publication1
Metal bindingi125Iron; via tele nitrogen; catalytic1 Publication1
Metal bindingi127Iron; catalytic1 Publication1
Binding sitei140Substrate1 Publication1
Metal bindingi187Iron; via tele nitrogen; catalytic1 Publication1
Binding sitei187Substrate1 Publication1

GO - Molecular functioni

GO - Biological processi

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

Keywords - Molecular functioni

Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11430-MONOMER.
ECOL316407:JW1114-MONOMER.
MetaCyc:EG11430-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
Mutagenesisi116S → A: Loss of binding of 2-oxoglutarate. 1 Publication1
Mutagenesisi140R → A: Loss of binding of 2-oxoglutarate. 1 Publication1
Mutagenesisi211I → R: Blocks dimerization. Loss of activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001688301 – 37350S ribosomal protein L16 3-hydroxylaseAdd BLAST373

Proteomic databases

EPDiP27431.
PaxDbiP27431.
PRIDEiP27431.

Interactioni

Subunit structurei

Homodimer.2 Publications

Protein-protein interaction databases

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

Structurei

Secondary structure

1373
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi9 – 15Combined sources7
Turni16 – 19Combined sources4
Beta strandi22 – 24Combined sources3
Beta strandi27 – 30Combined sources4
Helixi37 – 44Combined sources8
Beta strandi51 – 57Combined sources7
Beta strandi60 – 66Combined sources7
Beta strandi76 – 84Combined sources9
Helixi86 – 88Combined sources3
Helixi91 – 94Combined sources4
Helixi95 – 102Combined sources8
Helixi105 – 107Combined sources3
Beta strandi108 – 116Combined sources9
Beta strandi131 – 135Combined sources5
Beta strandi137 – 145Combined sources9
Beta strandi167 – 173Combined sources7
Beta strandi178 – 181Combined sources4
Beta strandi187 – 202Combined sources16
Helixi207 – 221Combined sources15
Helixi244 – 258Combined sources15
Helixi261 – 272Combined sources12
Helixi290 – 298Combined sources9
Beta strandi303 – 305Combined sources3
Beta strandi311 – 314Combined sources4
Beta strandi317 – 320Combined sources4
Beta strandi323 – 325Combined sources3
Helixi330 – 338Combined sources9
Beta strandi340 – 342Combined sources3
Helixi344 – 347Combined sources4
Helixi348 – 352Combined sources5
Helixi354 – 365Combined sources12
Beta strandi368 – 371Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini92 – 219JmjCPROSITE-ProRule annotationAdd BLAST128

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni125 – 127Substrate-binding1 Publication3

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.
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
PDB 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.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260093. 7 interactors.
DIPiDIP-11535N.
IntActiP27431. 12 interactors.
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.
PhylomeDBiP27431.

Enzyme and pathway databases

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

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: November 2, 2016
This is version 115 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.