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Protein

Decapping and exoribonuclease protein

Gene

DXO

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

Functioni

Ribonuclease that specifically degrades pre-mRNAs with a defective 5' end cap and is part of a pre-mRNA capping quality control. Has decapping, pyrophosphohydrolase and 5'-3' exonuclease activities. Has decapping activity toward incomplete 5' end cap mRNAs such as unmethylated 5' end-capped RNA to release GpppN and 5' end monophosphate RNA. The 5' end monophosphate RNA is then degraded by the 5'-3' exoribonuclease activity, enabling this enzyme to decap and degrade incompletely capped mRNAs. Also possesses RNA 5'-pyrophosphohydrolase activity by hydrolyzing the 5' end triphosphate to release pyrophosphates (By similarity).By similarity

Cofactori

Mg2+By similarityNote: Binds 2 magnesium ions.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei58 – 581SubstrateBy similarity
Binding sitei101 – 1011SubstrateBy similarity
Binding sitei132 – 1321SubstrateBy similarity
Metal bindingi192 – 1921Magnesium 1By similarity
Metal bindingi192 – 1921Magnesium 2By similarity
Binding sitei217 – 2171SubstrateBy similarity
Metal bindingi234 – 2341Magnesium 2By similarity
Binding sitei234 – 2341SubstrateBy similarity
Metal bindingi236 – 2361Magnesium 1By similarity
Metal bindingi236 – 2361Magnesium 2By similarity
Metal bindingi253 – 2531Magnesium 1By similarity
Metal bindingi254 – 2541Magnesium 1; via carbonyl oxygenBy similarity
Binding sitei280 – 2801SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Ligandi

Magnesium, Metal-binding, Nucleotide-binding, RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Decapping and exoribonuclease protein (EC:3.1.13.-, EC:3.6.1.-)
Short name:
DXO
Alternative name(s):
Dom-3 homolog Z
Gene namesi
Name:DXO
Synonyms:DOM3L, DOM3Z, NG6
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:2992. DXO.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA27458.

Polymorphism and mutation databases

BioMutaiDOM3Z.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 396396Decapping and exoribonuclease proteinPRO_0000249822Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei392 – 3921PhosphothreonineBy similarity
Modified residuei394 – 3941PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiO77932.
MaxQBiO77932.
PaxDbiO77932.
PRIDEiO77932.

PTM databases

PhosphoSiteiO77932.

Expressioni

Tissue specificityi

Ubiquitously expressed.1 Publication

Gene expression databases

BgeeiO77932.
CleanExiHS_DOM3Z.
ExpressionAtlasiO77932. baseline and differential.
GenevisibleiO77932. HS.

Organism-specific databases

HPAiHPA046708.

Interactioni

Protein-protein interaction databases

BioGridi108132. 15 interactions.
IntActiO77932. 8 interactions.
MINTiMINT-1034427.
STRINGi9606.ENSP00000337759.

Structurei

3D structure databases

ProteinModelPortaliO77932.
SMRiO77932. Positions 27-384.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the DXO/Dom3Z family.Curated

Phylogenomic databases

eggNOGiKOG1982. Eukaryota.
ENOG410ZAFR. LUCA.
GeneTreeiENSGT00390000006425.
HOVERGENiHBG080627.
InParanoidiO77932.
KOiK14845.
OMAiHSPGQWR.
PhylomeDBiO77932.
TreeFamiTF322812.

Family and domain databases

InterProiIPR013961. RAI1.
[Graphical view]
PfamiPF08652. RAI1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O77932-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDPRGTKRGA EKTEVAEPRN KLPRPAPSLP TDPALYSGPF PFYRRPSELG
60 70 80 90 100
CFSLDAQRQY HGDARALRYY SPPPTNGPGP NFDLRDGYPD RYQPRDEEVQ
110 120 130 140 150
ERLDHLLCWL LEHRGRLEGG PGWLAEAIVT WRGHLTKLLT TPYERQEGWQ
160 170 180 190 200
LAASRFQGTL YLSEVETPNA RAQRLARPPL LRELMYMGYK FEQYMCADKP
210 220 230 240 250
GSSPDPSGEV NTNVAFCSVL RSRLGSHPLL FSGEVDCTDP QAPSTQPPTC
260 270 280 290 300
YVELKTSKEM HSPGQWRSFY RHKLLKWWAQ SFLPGVPNVV AGFRNPDGFV
310 320 330 340 350
SSLKTFPTMK MFEYVRNDRD GWNPSVCMNF CAAFLSFAQS TVVQDDPRLV
360 370 380 390
HLFSWEPGGP VTVSVHQDAP YAFLPIWYVE AMTQDLPSPP KTPSPK
Length:396
Mass (Da):44,929
Last modified:September 19, 2006 - v2
Checksum:i17C8119037EB6892
GO

Sequence cautioni

The sequence AAB67983.1 differs from that shown. Reason: Erroneous gene model prediction. Curated
The sequence CAB89306.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti28 – 281S → T.2 Publications
Corresponds to variant rs1056694 [ dbSNP | Ensembl ].
VAR_027492
Natural varianti63 – 631D → E.
Corresponds to variant rs2746396 [ dbSNP | Ensembl ].
VAR_027493
Natural varianti261 – 2611H → Q.1 Publication
Corresponds to variant rs17207867 [ dbSNP | Ensembl ].
VAR_027494
Natural varianti332 – 3321A → V.
Corresponds to variant rs12205138 [ dbSNP | Ensembl ].
VAR_027495

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF059252 mRNA. Translation: AAC78603.1.
AF019413 Genomic DNA. Translation: AAB67983.1. Sequence problems.
AL049547 Genomic DNA. Translation: CAB89305.1.
AL049547 Genomic DNA. Translation: CAB89306.1. Sequence problems.
AL662849 Genomic DNA. Translation: CAI17465.1.
AL844853 Genomic DNA. Translation: CAI41864.1.
CR753822 Genomic DNA. Translation: CAM26055.1.
CR759782 Genomic DNA. Translation: CAQ07122.1.
AL645922 Genomic DNA. Translation: CAQ09281.1.
CR753845 Genomic DNA. Translation: CAQ10912.1.
CH471081 Genomic DNA. Translation: EAX03558.1.
BC009344 mRNA. Translation: AAH09344.1.
BC019083 mRNA. Translation: AAH19083.1.
AF059253 mRNA. Translation: AAC78604.1.
AF059254 mRNA. Translation: AAC78605.1.
CCDSiCCDS4732.1.
RefSeqiNP_005501.2. NM_005510.3.
XP_006715068.1. XM_006715005.2.
XP_006725537.1. XM_006725474.2.
XP_006725961.1. XM_006725898.2.
XP_006726048.1. XM_006725985.2.
XP_006726141.1. XM_006726078.2.
UniGeneiHs.153299.

Genome annotation databases

EnsembliENST00000337523; ENSP00000337759; ENSG00000204348.
ENST00000375349; ENSP00000364498; ENSG00000204348.
ENST00000375356; ENSP00000364505; ENSG00000204348.
ENST00000383330; ENSP00000372820; ENSG00000206346.
ENST00000399936; ENSP00000382818; ENSG00000206346.
ENST00000399937; ENSP00000382819; ENSG00000206346.
ENST00000414092; ENSP00000391123; ENSG00000236765.
ENST00000419797; ENSP00000391532; ENSG00000234798.
ENST00000426498; ENSP00000394167; ENSG00000225682.
ENST00000427627; ENSP00000413860; ENSG00000234798.
ENST00000427690; ENSP00000406143; ENSG00000225682.
ENST00000432110; ENSP00000401315; ENSG00000236765.
ENST00000439989; ENSP00000395262; ENSG00000224313.
ENST00000443250; ENSP00000415675; ENSG00000224313.
ENST00000446967; ENSP00000391349; ENSG00000234798.
ENST00000453742; ENSP00000410404; ENSG00000225682.
ENST00000454430; ENSP00000411380; ENSG00000224313.
ENST00000458308; ENSP00000400173; ENSG00000236765.
GeneIDi1797.
KEGGihsa:1797.
UCSCiuc003nyp.2. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF059252 mRNA. Translation: AAC78603.1.
AF019413 Genomic DNA. Translation: AAB67983.1. Sequence problems.
AL049547 Genomic DNA. Translation: CAB89305.1.
AL049547 Genomic DNA. Translation: CAB89306.1. Sequence problems.
AL662849 Genomic DNA. Translation: CAI17465.1.
AL844853 Genomic DNA. Translation: CAI41864.1.
CR753822 Genomic DNA. Translation: CAM26055.1.
CR759782 Genomic DNA. Translation: CAQ07122.1.
AL645922 Genomic DNA. Translation: CAQ09281.1.
CR753845 Genomic DNA. Translation: CAQ10912.1.
CH471081 Genomic DNA. Translation: EAX03558.1.
BC009344 mRNA. Translation: AAH09344.1.
BC019083 mRNA. Translation: AAH19083.1.
AF059253 mRNA. Translation: AAC78604.1.
AF059254 mRNA. Translation: AAC78605.1.
CCDSiCCDS4732.1.
RefSeqiNP_005501.2. NM_005510.3.
XP_006715068.1. XM_006715005.2.
XP_006725537.1. XM_006725474.2.
XP_006725961.1. XM_006725898.2.
XP_006726048.1. XM_006725985.2.
XP_006726141.1. XM_006726078.2.
UniGeneiHs.153299.

3D structure databases

ProteinModelPortaliO77932.
SMRiO77932. Positions 27-384.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi108132. 15 interactions.
IntActiO77932. 8 interactions.
MINTiMINT-1034427.
STRINGi9606.ENSP00000337759.

PTM databases

PhosphoSiteiO77932.

Polymorphism and mutation databases

BioMutaiDOM3Z.

Proteomic databases

EPDiO77932.
MaxQBiO77932.
PaxDbiO77932.
PRIDEiO77932.

Protocols and materials databases

DNASUi1797.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000337523; ENSP00000337759; ENSG00000204348.
ENST00000375349; ENSP00000364498; ENSG00000204348.
ENST00000375356; ENSP00000364505; ENSG00000204348.
ENST00000383330; ENSP00000372820; ENSG00000206346.
ENST00000399936; ENSP00000382818; ENSG00000206346.
ENST00000399937; ENSP00000382819; ENSG00000206346.
ENST00000414092; ENSP00000391123; ENSG00000236765.
ENST00000419797; ENSP00000391532; ENSG00000234798.
ENST00000426498; ENSP00000394167; ENSG00000225682.
ENST00000427627; ENSP00000413860; ENSG00000234798.
ENST00000427690; ENSP00000406143; ENSG00000225682.
ENST00000432110; ENSP00000401315; ENSG00000236765.
ENST00000439989; ENSP00000395262; ENSG00000224313.
ENST00000443250; ENSP00000415675; ENSG00000224313.
ENST00000446967; ENSP00000391349; ENSG00000234798.
ENST00000453742; ENSP00000410404; ENSG00000225682.
ENST00000454430; ENSP00000411380; ENSG00000224313.
ENST00000458308; ENSP00000400173; ENSG00000236765.
GeneIDi1797.
KEGGihsa:1797.
UCSCiuc003nyp.2. human.

Organism-specific databases

CTDi1797.
GeneCardsiDXO.
H-InvDBHIX0166417.
HGNCiHGNC:2992. DXO.
HPAiHPA046708.
MIMi605996. gene.
neXtProtiNX_O77932.
PharmGKBiPA27458.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1982. Eukaryota.
ENOG410ZAFR. LUCA.
GeneTreeiENSGT00390000006425.
HOVERGENiHBG080627.
InParanoidiO77932.
KOiK14845.
OMAiHSPGQWR.
PhylomeDBiO77932.
TreeFamiTF322812.

Miscellaneous databases

ChiTaRSiDXO. human.
GeneWikiiDOM3Z.
GenomeRNAii1797.
NextBioi7321.
PROiO77932.
SOURCEiSearch...

Gene expression databases

BgeeiO77932.
CleanExiHS_DOM3Z.
ExpressionAtlasiO77932. baseline and differential.
GenevisibleiO77932. HS.

Family and domain databases

InterProiIPR013961. RAI1.
[Graphical view]
PfamiPF08652. RAI1. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Four ubiquitously expressed genes, RD (D6S45)-SKI2W (SKIV2L)-DOM3Z-RP1 (D6S60E), are present between complement component genes factor B and C4 in the class III region of the HLA."
    Yang Z., Shen L., Dangel A.W., Wu L.-C., Yu C.Y.
    Genomics 53:338-347(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT THR-28, TISSUE SPECIFICITY.
  2. "Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse."
    Xie T., Rowen L., Aguado B., Ahearn M.E., Madan A., Qin S., Campbell R.D., Hood L.
    Genome Res. 13:2621-2636(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT GLN-261.
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Neuroblastoma and Retinoblastoma.
  6. "Organizations and gene duplications of the human and mouse MHC complement gene clusters."
    Yang Z., Yu C.Y.
    Exp. Clin. Immunogenet. 17:1-17(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1-106, VARIANT THR-28.
  7. "Unraveling regulation and new components of human P-bodies through a protein interaction framework and experimental validation."
    Zheng D., Chen C.Y., Shyu A.B.
    RNA 17:1619-1634(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION.

Entry informationi

Entry nameiDXO_HUMAN
AccessioniPrimary (citable) accession number: O77932
Secondary accession number(s): A2CER3
, B0UZ80, O15004, O78127, O78128, Q5ST60, Q6IPZ2, Q9NPK4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 19, 2006
Last sequence update: September 19, 2006
Last modified: March 16, 2016
This is version 112 of the entry and version 2 of the sequence. [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

Caution

In contrast to canonical decapping enzymes DCP2 and NUDT16, which release m7pppG (m7GDP), the decapping activity releases the entire cap structure GpppN and a 5' end monophosphate RNA.Curated

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: 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. 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.