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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)DescriptionActionsGraphical viewLength
Binding sitei98SubstrateUniRule annotation1
Binding sitei101SubstrateUniRule annotation1
Active sitei154Proton acceptorUniRule annotation1
Metal bindingi162ZincUniRule annotation1
Metal bindingi165ZincUniRule annotation1
Metal bindingi203ZincUniRule annotation1
Metal bindingi208ZincUniRule annotation1
Binding sitei289NAD; via amide nitrogenUniRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi54 – 73NADUniRule annotationAdd BLAST20
Nucleotide bindingi136 – 139NADUniRule annotation4
Nucleotide bindingi245 – 247NADUniRule annotation3
Nucleotide bindingi271 – 273NADUniRule annotation3

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)DescriptionActionsGraphical viewLength
Transit peptidei1 – 32MitochondrionUniRule annotationAdd BLAST32
ChainiPRO_000041557333 – 305NAD-dependent protein deacylase sirtuin-5, mitochondrialAdd BLAST273

Proteomic databases

PaxDbiQ6DHI5.
PRIDEiQ6DHI5.

Expressioni

Gene expression databases

BgeeiENSDARG00000039684.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000040792.

Structurei

Secondary structure

1305
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi36 – 45Combined sources10
Beta strandi47 – 53Combined sources7
Helixi55 – 59Combined sources5
Turni60 – 62Combined sources3
Helixi78 – 81Combined sources4
Helixi84 – 89Combined sources6
Helixi91 – 104Combined sources14
Helixi105 – 107Combined sources3
Helixi112 – 126Combined sources15
Beta strandi130 – 135Combined sources6
Helixi141 – 144Combined sources4
Beta strandi149 – 152Combined sources4
Beta strandi155 – 162Combined sources8
Turni163 – 165Combined sources3
Beta strandi168 – 170Combined sources3
Beta strandi174 – 177Combined sources4
Helixi178 – 180Combined sources3
Helixi197 – 199Combined sources3
Turni206 – 208Combined sources3
Beta strandi211 – 216Combined sources6
Helixi225 – 237Combined sources13
Beta strandi239 – 246Combined sources8
Beta strandi248 – 250Combined sources3
Helixi253 – 255Combined sources3
Helixi257 – 262Combined sources6
Beta strandi267 – 272Combined sources6
Beta strandi283 – 287Combined sources5
Helixi289 – 297Combined sources9

3D structure databases

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

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini37 – 305Deacetylase sirtuin-typeUniRule annotationAdd BLAST269

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.
GeneTreeiENSGT00850000132288.
HOGENOMiHOG000085950.
HOVERGENiHBG056009.
InParanoidiQ6DHI5.
KOiK11415.
OMAiLIHMHGE.
OrthoDBiEOG091G0KF2.
PhylomeDBiQ6DHI5.
TreeFamiTF106183.

Family and domain databases

CDDicd01412. SIRT5_Af1_CobB. 1 hit.
Gene3Di3.30.1600.10. 2 hits.
3.40.50.1220. 3 hits.
HAMAPiMF_01121. Sirtuin_ClassIII. 1 hit.
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
PDB 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.
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.
GeneTreeiENSGT00850000132288.
HOGENOMiHOG000085950.
HOVERGENiHBG056009.
InParanoidiQ6DHI5.
KOiK11415.
OMAiLIHMHGE.
OrthoDBiEOG091G0KF2.
PhylomeDBiQ6DHI5.
TreeFamiTF106183.

Miscellaneous databases

PROiQ6DHI5.

Gene expression databases

BgeeiENSDARG00000039684.

Family and domain databases

CDDicd01412. SIRT5_Af1_CobB. 1 hit.
Gene3Di3.30.1600.10. 2 hits.
3.40.50.1220. 3 hits.
HAMAPiMF_01121. Sirtuin_ClassIII. 1 hit.
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...

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 2, 2016
This is version 96 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.