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Protein

E3 ubiquitin-protein ligase Arkadia

Gene

RNF111

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

E3 ubiquitin-protein ligase (PubMed:26656854). Required for mesoderm patterning during embryonic development (By similarity). Acts as an enhancer of the transcriptional responses of the SMAD2/SMAD3 effectors, which are activated downstream of BMP (PubMed:14657019, PubMed:16601693). Acts by mediating ubiquitination and degradation of SMAD inhibitors such as SMAD7, inducing their proteasomal degradation and thereby enhancing the transcriptional activity of TGF-beta and BMP (PubMed:14657019, PubMed:16601693). In addition to enhance transcription of SMAD2/SMAD3 effectors, also regulates their turnover by mediating their ubiquitination and subsequent degradation, coupling their activation with degradation, thereby ensuring that only effectors 'in use' are degraded (By similarity). Activates SMAD3/SMAD4-dependent transcription by triggering signal-induced degradation of SNON isoform of SKIL (PubMed:17591695). Associates with UBE2D2 as an E2 enzyme (PubMed:22411132). Specifically binds polysumoylated chains via SUMO interaction motifs (SIMs) and mediates ubiquitination of sumoylated substrates (PubMed:23751493). Catalyzes 'Lys-63'-linked ubiquitination of sumoylated XPC in response to UV irradiation, promoting nucleotide excision repair (PubMed:23751493). Mediates ubiquitination and degradation of sumoylated PML (By similarity). The regulation of the BMP-SMAD signaling is however independent of sumoylation and is not dependent of SUMO interaction motifs (SIMs) (By similarity).By similarity6 Publications

Catalytic activityi

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.1 Publication

Enzyme regulationi

Binds free ubiquitin non-covalently via its RING-type zinc finger. Ubiquitin-binding leads to enhance the E3 ubiquitin-protein ligase activity by stabilizing the ubiquitin-conjugating enzyme E2 (donor ubiquitin) in the 'closed' conformation and activating ubiquitin transfer.By similarity

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.6 Publications
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi942ZincBy similarity1
Metal bindingi945ZincBy similarity1
Metal bindingi965ZincBy similarity1
Metal bindingi968ZincBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri942 – 983RING-type; atypicalPROSITE-ProRule annotationAdd BLAST42

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • SMAD binding Source: Ensembl
  • SUMO polymer binding Source: UniProtKB
  • ubiquitin protein ligase activity Source: BHF-UCL

GO - Biological processi

Keywordsi

Molecular functionDevelopmental protein, Transferase
Biological processDNA damage, DNA repair, Ubl conjugation pathway
LigandMetal-binding, Zinc

Enzyme and pathway databases

BRENDAi6.3.2.19. 2681.
ReactomeiR-HSA-2173795. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
R-HSA-2173796. SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription.
R-HSA-5696395. Formation of Incision Complex in GG-NER.
R-HSA-983168. Antigen processing: Ubiquitination & Proteasome degradation.
SignaLinkiQ6ZNA4.
SIGNORiQ6ZNA4.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase Arkadia1 Publication (EC:2.3.2.271 Publication)
Alternative name(s):
RING finger protein 111Imported
Short name:
hRNF1111 Publication
RING-type E3 ubiquitin transferase ArkadiaCurated
Gene namesi
Name:RNF111Imported
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 15

Organism-specific databases

EuPathDBiHostDB:ENSG00000157450.15.
HGNCiHGNC:17384. RNF111.

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi300 – 303VVVI → AAAA or AVAA: Abolishes binding to sumoylated proteins and ubiquitination and degradation of XPC; when associated with 326-A--A-329 and 382-A--A-385. 1 Publication4
Mutagenesisi326 – 329VEIV → AAAA or AEAA: Abolishes binding to sumoylated proteins and ubiquitination and degradation of XPC; when associated with 300-A--A-303 and 382-A--A-385. 1 Publication4
Mutagenesisi382 – 385VVDL → AAAA or AADA: Abolishes binding to sumoylated proteins and ubiquitination and degradation of XPC; when associated with 300-A--A-303 and 326-A--A-329. 1 Publication4
Mutagenesisi382V → A: Abolishes SUMO binding. 1 Publication1
Mutagenesisi382V → L: Loss of affinity to SUMO1 and SUMO2. 1 Publication1
Mutagenesisi382V → Y: No loss of affinity toward SUMO1 and SUMO2. 1 Publication1
Mutagenesisi383V → A: Abolishes SUMO binding. 1 Publication1
Mutagenesisi383V → I: No loss of affinity toward SUMO1 and SUMO2. 1 Publication1
Mutagenesisi384D → A: Abolishes SUMO binding. 1 Publication1
Mutagenesisi384D → E: Loss of affinity to SUMO1 and SUMO2. 1 Publication1
Mutagenesisi384D → N: Loss of affinity to SUMO1 and SUMO2. 1 Publication1
Mutagenesisi385L → A: Abolishes SUMO binding. 1 Publication1
Mutagenesisi385L → I: Loss of affinity to SUMO1 and SUMO2. 1 Publication1
Mutagenesisi386T → A: Abolishes SUMO binding. 1 Publication1
Mutagenesisi386T → S: Loss of affinity to SUMO1 and SUMO2. 1 Publication1
Mutagenesisi386T → V: Loss of affinity to SUMO1 and SUMO2. 1 Publication1

Organism-specific databases

DisGeNETi54778.
OpenTargetsiENSG00000157450.
PharmGKBiPA134868772.

Polymorphism and mutation databases

BioMutaiRNF111.
DMDMi308153555.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002806901 – 994E3 ubiquitin-protein ligase ArkadiaAdd BLAST994

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki19Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki28Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki34Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki47Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki59Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki73Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki87Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki96Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki110Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki173Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki198Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki218Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki923Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki927Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

EPDiQ6ZNA4.
MaxQBiQ6ZNA4.
PaxDbiQ6ZNA4.
PeptideAtlasiQ6ZNA4.
PRIDEiQ6ZNA4.

PTM databases

iPTMnetiQ6ZNA4.
PhosphoSitePlusiQ6ZNA4.

Expressioni

Tissue specificityi

Broadly expressed.1 Publication

Gene expression databases

BgeeiENSG00000157450.
CleanExiHS_RNF111.
ExpressionAtlasiQ6ZNA4. baseline and differential.
GenevisibleiQ6ZNA4. HS.

Organism-specific databases

HPAiHPA038576.
HPA038577.

Interactioni

Subunit structurei

Monomer (PubMed:26656854). Interacts with SMAD6, SMAD7, AXIN1, AXIN2 and SKIL isoform SNON (PubMed:16601693, PubMed:17591695). Interacts with (phosphorylated) SMAD2 and SMAD3 (By similarity). Part of a complex containing RNF111, AXIN1 and SMAD7 (PubMed:16601693). Interacts (via SIM domains) with SUMO1 and SUMO2 (PubMed:23086935).By similarity4 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • SMAD binding Source: Ensembl
  • SUMO polymer binding Source: UniProtKB

Protein-protein interaction databases

BioGridi120146. 71 interactors.
IntActiQ6ZNA4. 38 interactors.
MINTiMINT-1187466.
STRINGi9606.ENSP00000288199.

Structurei

Secondary structure

1994
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni943 – 946Combined sources4
Beta strandi951 – 953Combined sources3
Beta strandi955 – 957Combined sources3
Beta strandi963 – 965Combined sources3
Helixi966 – 975Combined sources10
Turni980 – 982Combined sources3
Beta strandi984 – 986Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2KIZNMR-A927-994[»]
5LG0NMR-A927-994[»]
5LG7NMR-A927-994[»]
ProteinModelPortaliQ6ZNA4.
SMRiQ6ZNA4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni241 – 404Interaction with AXIN11 PublicationAdd BLAST164
Regioni907 – 909Ubiquitin bindingBy similarity3
Regioni957 – 961Ubiquitin bindingBy similarity5

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi300 – 304SUMO interaction motif 1 (SIM)2 Publications5
Motifi325 – 331SUMO interaction motif 2 (SIM)2 Publications7
Motifi382 – 386SUMO interaction motif 3 (SIM)2 Publications5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi252 – 464Ser-richAdd BLAST213
Compositional biasi494 – 523His-richAdd BLAST30
Compositional biasi629 – 781Pro-richAdd BLAST153

Domaini

The SUMO interaction motifs (SIMs) mediates the binding to polysumoylated substrate.2 Publications
The RING-type zinc finger mediates the E3 ubiquitin-protein ligase activity and binds directly to free ubiquitin (PubMed:26656854). Non-covalent ubiquitin-binding stabilizes the ubiquitin-conjugating enzyme E2 (donor ubiquitin) in the 'closed' conformation and stimulates ubiquitin transfer (By similarity).By similarity1 Publication

Sequence similaritiesi

Belongs to the Arkadia family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri942 – 983RING-type; atypicalPROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0800. Eukaryota.
ENOG41121N2. LUCA.
GeneTreeiENSGT00730000110863.
HOVERGENiHBG093884.
InParanoidiQ6ZNA4.
KOiK10635.
OMAiQPLRQNA.
OrthoDBiEOG091G0WPK.
PhylomeDBiQ6ZNA4.
TreeFamiTF331862.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiView protein in InterPro
IPR029306. RNF111_N.
IPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
PfamiView protein in Pfam
PF15303. RNF111_N. 1 hit.
PF13639. zf-RING_2. 1 hit.
SMARTiView protein in SMART
SM00184. RING. 1 hit.
PROSITEiView protein in PROSITE
PS50089. ZF_RING_2. 1 hit.

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q6ZNA4-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MSQWTPEYNE LYTLKVDMKS EIPSDAPKTQ ESLKGILLHP EPIGAAKSFP
60 70 80 90 100
AGVEMINSKV GNEFSHLCDD SQKQEKEMNG NQQEQEKSLV VRKKRKSQQA
110 120 130 140 150
GPSYVQNCVK ENQGILGLRQ HLGTPSDEDN DSSFSDCLSS PSSSLHFGDS
160 170 180 190 200
DTVTSDEDKE VSVRHSQTIL NAKSRSHSAR SHKWPRTETE SVSGLLMKRP
210 220 230 240 250
CLHGSSLRRL PCRKRFVKNN SSQRTQKQKE RILMQRKKRE VLARRKYALL
260 270 280 290 300
PSSSSSSEND LSSESSSSSS TEGEEDLFVS ASENHQNNPA VPSGSIDEDV
310 320 330 340 350
VVIEASSTPQ VTANEEINVT STDSEVEIVT VGESYRSRST LGHSRSHWSQ
360 370 380 390 400
GSSSHASRPQ EPRNRSRIST VIQPLRQNAA EVVDLTVDED EPTVVPTTSA
410 420 430 440 450
RMESQATSAS INNSNPSTSE QASDTASAVT SSQPSTVSET SATLTSNSTT
460 470 480 490 500
GTSIGDDSRR TTSSAVTETG PPAMPRLPSC CPQHSPCGGS SQNHHALGHP
510 520 530 540 550
HTSCFQQHGH HFQHHHHHHH TPHPAVPVSP SFSDPACPVE RPPQVQAPCG
560 570 580 590 600
ANSSSGTSYH EQQALPVDLS NSGIRSHGSG SFHGASAFDP CCPVSSSRAA
610 620 630 640 650
IFGHQAAAAA PSQPLSSIDG YGSSMVAQPQ PQPPPQPSLS SCRHYMPPPY
660 670 680 690 700
ASLTRPLHHQ ASACPHSHGN PPPQTQPPPQ VDYVIPHPVH AFHSQISSHA
710 720 730 740 750
TSHPVAPPPP THLASTAAPI PQHLPPTHQP ISHHIPATAP PAQRLHPHEV
760 770 780 790 800
MQRMEVQRRR MMQHPTRAHE RPPPHPHRMH PNYGHGHHIH VPQTMSSHPR
810 820 830 840 850
QAPERSAWEL GIEAGVTAAT YTPGALHPHL AHYHAPPRLH HLQLGALPLM
860 870 880 890 900
VPDMAGYPHI RYISSGLDGT SFRGPFRGNF EELIHLEERL GNVNRGASQG
910 920 930 940 950
TIERCTYPHK YKKVTTDWFS QRKLHCKQDG EEGTEEDTEE KCTICLSILE
960 970 980 990
EGEDVRRLPC MHLFHQVCVD QWLITNKKCP ICRVDIEAQL PSES
Length:994
Mass (Da):108,862
Last modified:October 5, 2010 - v3
Checksum:i7E387321E5F61FAB
GO
Isoform 2 (identifier: Q6ZNA4-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     914-921: Missing.

Show »
Length:986
Mass (Da):107,896
Checksum:iBD07D5D2C2B6AEB4
GO
Isoform 3 (identifier: Q6ZNA4-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     766-766: T → TGLFVFCVSR

Note: No experimental confirmation available.
Show »
Length:1,003
Mass (Da):109,871
Checksum:i9F0D0B05B5EB39A8
GO
Isoform 4 (identifier: Q6ZNA4-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     766-766: T → TGLFVFCVSR
     914-921: Missing.

Note: No experimental confirmation available.
Show »
Length:995
Mass (Da):108,906
Checksum:iA648717F19CFB655
GO

Sequence cautioni

The sequence AAH10369 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAC04531 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BAD18633 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti165H → R in BX647259 (PubMed:17974005).Curated1
Sequence conflicti473A → E in CAD98031 (PubMed:17974005).Curated1
Sequence conflicti562Missing in AAH60862 (PubMed:16572171).Curated1
Sequence conflicti562Missing in AAH20984 (PubMed:16572171).Curated1
Sequence conflicti625M → T in BX647259 (PubMed:17974005).Curated1
Sequence conflicti738T → I in BX647259 (PubMed:17974005).Curated1
Sequence conflicti809E → G in CAD98031 (PubMed:17974005).Curated1
Sequence conflicti931E → G in CAD98031 (PubMed:17974005).Curated1
Sequence conflicti938T → A in BX647259 (PubMed:17974005).Curated1
Sequence conflicti974I → V in BAD18471 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_0311859N → K3 PublicationsCorresponds to variant dbSNP:rs2899642Ensembl.1
Natural variantiVAR_057216718A → T. Corresponds to variant dbSNP:rs34086812Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_023840766T → TGLFVFCVSR in isoform 3 and isoform 4. 2 Publications1
Alternative sequenceiVSP_023841914 – 921Missing in isoform 2 and isoform 4. 2 Publications8

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK095327 mRNA. Translation: BAC04531.1. Different initiation.
AK131304 mRNA. Translation: BAD18471.1.
AK131488 mRNA. Translation: BAD18633.1. Different initiation.
AL157474 mRNA. Translation: CAB75669.2.
BX538130 mRNA. Translation: CAD98031.1.
BX647259 mRNA. No translation available.
AC025918 Genomic DNA. No translation available.
AC090515 Genomic DNA. No translation available.
AC092757 Genomic DNA. No translation available.
CH471082 Genomic DNA. Translation: EAW77561.1.
BC010369 mRNA. Translation: AAH10369.1. Different initiation.
BC020984 mRNA. Translation: AAH20984.1.
BC060862 mRNA. Translation: AAH60862.1.
CCDSiCCDS10169.1. [Q6ZNA4-2]
CCDS58365.1. [Q6ZNA4-4]
CCDS58366.1. [Q6ZNA4-1]
CCDS81888.1. [Q6ZNA4-3]
PIRiT46904.
RefSeqiNP_001257457.1. NM_001270528.1. [Q6ZNA4-4]
NP_001257458.1. NM_001270529.1.
NP_001257459.1. NM_001270530.1. [Q6ZNA4-1]
NP_001317260.1. NM_001330331.1. [Q6ZNA4-3]
NP_060080.6. NM_017610.7. [Q6ZNA4-2]
XP_006720642.1. XM_006720579.3. [Q6ZNA4-3]
XP_016877827.1. XM_017022338.1. [Q6ZNA4-1]
UniGeneiHs.404423.
Hs.603489.
Hs.741727.

Genome annotation databases

EnsembliENST00000348370; ENSP00000288199; ENSG00000157450. [Q6ZNA4-2]
ENST00000557998; ENSP00000452732; ENSG00000157450. [Q6ZNA4-1]
ENST00000559209; ENSP00000453872; ENSG00000157450. [Q6ZNA4-4]
ENST00000561186; ENSP00000453015; ENSG00000157450. [Q6ZNA4-3]
GeneIDi54778.
KEGGihsa:54778.
UCSCiuc002afs.5. human. [Q6ZNA4-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiRN111_HUMAN
AccessioniPrimary (citable) accession number: Q6ZNA4
Secondary accession number(s): C9JUS4
, H0YN55, Q6P9A4, Q6ZMU2, Q7L428, Q7Z346, Q8N1P9, Q8WUA3, Q9NSR1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 20, 2007
Last sequence update: October 5, 2010
Last modified: October 25, 2017
This is version 139 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 15
    Human chromosome 15: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families