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Protein

NAD-dependent protein deacylase sirtuin-5, mitochondrial

Gene

sirt5

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

NAD-dependent lysine demalonylase, desuccinylase and deglutarylase that specifically removes malonyl, succinyl and glutaryl groups on target proteins. Has weak NAD-dependent protein deacetylase activity; however this activity may not be physiologically relevant in vivo.UniRule annotation

Catalytic activityi

NAD+ + a malonylprotein = nicotinamide + O-malonyl-ADP-ribose + a protein.UniRule annotation
NAD+ + a succinylprotein = nicotinamide + O-succinyl-ADP-ribose + a protein.UniRule annotation
NAD+ + a glutarylprotein = nicotinamide + O-glutaryl-ADP-ribose + a protein.UniRule annotation

Cofactori

Zn2+UniRule annotationNote: Binds 1 zinc ion per subunit.UniRule annotation

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei98 – 981SubstrateUniRule annotation
Binding sitei101 – 1011SubstrateUniRule annotation
Active sitei154 – 1541Proton acceptorUniRule annotation
Metal bindingi162 – 1621ZincUniRule annotation
Metal bindingi165 – 1651ZincUniRule annotation
Metal bindingi203 – 2031ZincUniRule annotation
Metal bindingi208 – 2081ZincUniRule annotation
Binding sitei289 – 2891NAD; via amide nitrogenUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi54 – 7320NADUniRule annotationAdd
BLAST
Nucleotide bindingi136 – 1394NADUniRule annotation
Nucleotide bindingi245 – 2473NADUniRule annotation
Nucleotide bindingi271 – 2733NADUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Ligandi

Metal-binding, NAD, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
NAD-dependent protein deacylase sirtuin-5, mitochondrialUniRule annotation (EC:3.5.1.-UniRule annotation)
Alternative name(s):
Regulatory protein SIR2 homolog 5UniRule annotation
Gene namesi
Name:sirt5
ORF Names:si:ch211-121a2.1
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 20

Organism-specific databases

ZFINiZDB-GENE-040718-349. sirt5.

Subcellular locationi

  • Mitochondrion UniRule annotation
  • Cytoplasmcytosol UniRule annotation
  • Nucleus UniRule annotation

  • Note: Mainly mitochondrial. Also present extramitochondrially: a fraction is present in the cytosol and very small amounts are also detected in the nucleus.UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Mitochondrion, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 3232MitochondrionUniRule annotationAdd
BLAST
Chaini33 – 305273NAD-dependent protein deacylase sirtuin-5, mitochondrialPRO_0000415573Add
BLAST

Proteomic databases

PaxDbiQ6DHI5.
PRIDEiQ6DHI5.

Expressioni

Gene expression databases

BgeeiQ6DHI5.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000040792.

Structurei

Secondary structure

1
305
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi36 – 4510Combined sources
Beta strandi47 – 537Combined sources
Helixi55 – 595Combined sources
Turni60 – 623Combined sources
Helixi78 – 814Combined sources
Helixi84 – 896Combined sources
Helixi91 – 10414Combined sources
Helixi105 – 1073Combined sources
Helixi112 – 12615Combined sources
Beta strandi130 – 1356Combined sources
Helixi141 – 1444Combined sources
Beta strandi149 – 1524Combined sources
Beta strandi155 – 1628Combined sources
Turni163 – 1653Combined sources
Beta strandi168 – 1703Combined sources
Beta strandi174 – 1774Combined sources
Helixi178 – 1803Combined sources
Helixi197 – 1993Combined sources
Turni206 – 2083Combined sources
Beta strandi211 – 2166Combined sources
Helixi225 – 23713Combined sources
Beta strandi239 – 2468Combined sources
Beta strandi248 – 2503Combined sources
Helixi253 – 2553Combined sources
Helixi257 – 2626Combined sources
Beta strandi267 – 2726Combined sources
Beta strandi283 – 2875Combined sources
Helixi289 – 2979Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4UTNX-ray3.00A/B30-298[»]
4UTRX-ray2.90A/B30-298[»]
4UTVX-ray2.40A/B30-298[»]
4UTXX-ray3.10A/B30-298[»]
4UTZX-ray3.30A/B30-298[»]
4UU7X-ray3.00A/B30-298[»]
4UU8X-ray2.90A/B30-298[»]
4UUAX-ray2.80A/B30-298[»]
4UUBX-ray2.90A/B30-298[»]
ProteinModelPortaliQ6DHI5.
SMRiQ6DHI5. Positions 32-297.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini37 – 305269Deacetylase sirtuin-typeUniRule annotationAdd
BLAST

Domaini

In contrast to class I sirtuins, class III sirtuins have only weak deacetylase activity. Difference in substrate specificity is probably due to a larger hydrophobic pocket with 2 residues (Tyr-98 and Arg-101) that bind to malonylated and succinylated substrates and define the specificity.UniRule annotation

Sequence similaritiesi

Belongs to the sirtuin family. Class III subfamily.UniRule annotation
Contains 1 deacetylase sirtuin-type domain.UniRule annotation

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG2684. Eukaryota.
COG0846. LUCA.
GeneTreeiENSGT00740000115330.
HOGENOMiHOG000085950.
HOVERGENiHBG056009.
InParanoidiQ6DHI5.
KOiK11415.
OMAiLIHMHGE.
OrthoDBiEOG77Q4XG.
PhylomeDBiQ6DHI5.
TreeFamiTF106183.

Family and domain databases

Gene3Di3.30.1600.10. 2 hits.
3.40.50.1220. 3 hits.
HAMAPiMF_01121. Sirtuin_ClassIII.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR003000. Sirtuin.
IPR026591. Sirtuin_cat_small_dom.
IPR027546. Sirtuin_class_III.
IPR026590. Ssirtuin_cat_dom.
[Graphical view]
PANTHERiPTHR11085. PTHR11085. 1 hit.
PfamiPF02146. SIR2. 1 hit.
[Graphical view]
SUPFAMiSSF52467. SSF52467. 1 hit.
PROSITEiPS50305. SIRTUIN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q6DHI5-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MIVRQLWCSR GSTSHLCAAV RLNWRSPKMT RPSSDLTAFR EHFAKAKHIA
60 70 80 90 100
IITGAGVSAE SGVPTFRGPG GFWRKWQAQD LATPEAFSRD PSLVWEFYHY
110 120 130 140 150
RREVMRSKMP NPAHLAIAEC EARLGQQGRS VVIITQNIDE LHHRAGSKHV
160 170 180 190 200
YEIHGSLFKT RCMSCGEVKA NHKSPICPAL DGKGAPDPNT KEARIPVELL
210 220 230 240 250
PRCERKSCNG LLRPHVVWFG ETLDSDILTA VERELEKCDL CLVVGTSSIV
260 270 280 290 300
YPAAMFAPQV ASRGVPVAEF NMECTPATQR FKYHFEGPCG STLPPALERH

ESEAV
Length:305
Mass (Da):33,929
Last modified:August 16, 2004 - v1
Checksum:iDF76E09F9396B8F4
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX511260 Genomic DNA. Translation: CAP09604.1.
BC075987 mRNA. Translation: AAH75987.1.
RefSeqiNP_001002605.1. NM_001002605.1.
UniGeneiDr.80771.

Genome annotation databases

EnsembliENSDART00000040793; ENSDARP00000040792; ENSDARG00000039684.
GeneIDi436878.
KEGGidre:436878.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BX511260 Genomic DNA. Translation: CAP09604.1.
BC075987 mRNA. Translation: AAH75987.1.
RefSeqiNP_001002605.1. NM_001002605.1.
UniGeneiDr.80771.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4UTNX-ray3.00A/B30-298[»]
4UTRX-ray2.90A/B30-298[»]
4UTVX-ray2.40A/B30-298[»]
4UTXX-ray3.10A/B30-298[»]
4UTZX-ray3.30A/B30-298[»]
4UU7X-ray3.00A/B30-298[»]
4UU8X-ray2.90A/B30-298[»]
4UUAX-ray2.80A/B30-298[»]
4UUBX-ray2.90A/B30-298[»]
ProteinModelPortaliQ6DHI5.
SMRiQ6DHI5. Positions 32-297.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000040792.

Proteomic databases

PaxDbiQ6DHI5.
PRIDEiQ6DHI5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000040793; ENSDARP00000040792; ENSDARG00000039684.
GeneIDi436878.
KEGGidre:436878.

Organism-specific databases

CTDi23408.
ZFINiZDB-GENE-040718-349. sirt5.

Phylogenomic databases

eggNOGiKOG2684. Eukaryota.
COG0846. LUCA.
GeneTreeiENSGT00740000115330.
HOGENOMiHOG000085950.
HOVERGENiHBG056009.
InParanoidiQ6DHI5.
KOiK11415.
OMAiLIHMHGE.
OrthoDBiEOG77Q4XG.
PhylomeDBiQ6DHI5.
TreeFamiTF106183.

Miscellaneous databases

NextBioi20831306.
PROiQ6DHI5.

Gene expression databases

BgeeiQ6DHI5.

Family and domain databases

Gene3Di3.30.1600.10. 2 hits.
3.40.50.1220. 3 hits.
HAMAPiMF_01121. Sirtuin_ClassIII.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR003000. Sirtuin.
IPR026591. Sirtuin_cat_small_dom.
IPR027546. Sirtuin_class_III.
IPR026590. Ssirtuin_cat_dom.
[Graphical view]
PANTHERiPTHR11085. PTHR11085. 1 hit.
PfamiPF02146. SIR2. 1 hit.
[Graphical view]
SUPFAMiSSF52467. SSF52467. 1 hit.
PROSITEiPS50305. SIRTUIN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  2. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (JUL-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

Entry informationi

Entry nameiSIR5_DANRE
AccessioniPrimary (citable) accession number: Q6DHI5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 22, 2012
Last sequence update: August 16, 2004
Last modified: November 11, 2015
This is version 92 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. 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.