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NAD-dependent protein deacylase Sir2 (EC 3.5.1.-) (Regulatory protein SIR2 homolog)

 NDP_MYCS2               Reviewed;         240 AA.
A0R2N3;
19-MAR-2014, integrated into UniProtKB/Swiss-Prot.
09-JAN-2007, sequence version 1.
10-OCT-2018, entry version 91.
RecName: Full=NAD-dependent protein deacylase Sir2 {ECO:0000255|HAMAP-Rule:MF_01121};
EC=3.5.1.- {ECO:0000255|HAMAP-Rule:MF_01121};
AltName: Full=Regulatory protein SIR2 homolog {ECO:0000255|HAMAP-Rule:MF_01121};
Name=sir2; Synonyms=cobB, npdA;
OrderedLocusNames=MSMEG_5175, MSMEI_5041;
Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycolicibacterium.
NCBI_TaxID=246196;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
Fraser C.M.;
Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
"Interrupted coding sequences in Mycobacterium smegmatis: authentic
mutations or sequencing errors?";
Genome Biol. 8:R20.1-R20.9(2007).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 700084 / mc(2)155;
PubMed=18955433; DOI=10.1101/gr.081901.108;
Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
"Ortho-proteogenomics: multiple proteomes investigation through
orthology and a new MS-based protocol.";
Genome Res. 19:128-135(2009).
[4]
PROTEIN SEQUENCE OF 71-94 AND 219-231, FUNCTION IN NHEJ, INTERACTION
WITH KU, SUBUNIT, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC 700084 / mc(2)155;
PubMed=21637345; DOI=10.1371/journal.pone.0020045;
Li Z., Wen J., Lin Y., Wang S., Xue P., Zhang Z., Zhou Y., Wang X.,
Sui L., Bi L.J., Zhang X.E.;
"A Sir2-like protein participates in mycobacterial NHEJ.";
PLoS ONE 6:E20045-E20045(2011).
-!- FUNCTION: NAD-dependent lysine deacetylase and desuccinylase that
specifically removes acetyl and succinyl groups on target
proteins. Modulates the activities of several proteins which are
inactive in their acylated form. {ECO:0000255|HAMAP-
Rule:MF_01121}.
-!- FUNCTION: Involved in non-homologous end joining (NHEJ) repair of
blunt, 5' overhang and 3' overhang DNA double strand breaks (DSB).
Overexpression increases the efficiency of NHEJ of the above DSBs
2-fold with no effect on repair fidelity.
{ECO:0000269|PubMed:21637345}.
-!- CATALYTIC ACTIVITY: NAD(+) + a succinylprotein = nicotinamide + O-
succinyl-ADP-ribose + a protein. {ECO:0000255|HAMAP-
Rule:MF_01121}.
-!- CATALYTIC ACTIVITY: NAD(+) + an acetylprotein = nicotinamide + O-
acetyl-ADP-ribose + a protein. {ECO:0000255|HAMAP-Rule:MF_01121}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000255|HAMAP-Rule:MF_01121};
Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-
Rule:MF_01121};
-!- SUBUNIT: Interacts with both Ku and LigD; may form a trimeric
complex during NHEJ. {ECO:0000269|PubMed:21637345}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01121}.
-!- DOMAIN: 2 residues (Tyr-53 and Arg-56) present in a large
hydrophobic pocket are probably involved in substrate specificity.
They are important for desuccinylation activity, but dispensable
for deacetylation activity. {ECO:0000255|HAMAP-Rule:MF_01121}.
-!- DISRUPTION PHENOTYPE: Not essential for growth in the absence of
DNA damage. Increased sensitivity to ionizing radiation in log,
stationary and late stationary phase. Decreased efficiency of NHEJ
on blunt, 5' overhang and 3' overhanging DSB, fidelity the same as
for wild-type NHEJ. {ECO:0000269|PubMed:21637345}.
-!- SIMILARITY: Belongs to the sirtuin family. Class III subfamily.
{ECO:0000255|HAMAP-Rule:MF_01121}.
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EMBL; CP000480; ABK72526.1; -; Genomic_DNA.
EMBL; CP001663; AFP41485.1; -; Genomic_DNA.
RefSeq; WP_011730361.1; NZ_CP009494.1.
RefSeq; YP_889421.1; NC_008596.1.
ProteinModelPortal; A0R2N3; -.
SMR; A0R2N3; -.
STRING; 246196.MSMEG_5175; -.
EnsemblBacteria; ABK72526; ABK72526; MSMEG_5175.
EnsemblBacteria; AFP41485; AFP41485; MSMEI_5041.
GeneID; 4534926; -.
KEGG; msb:LJ00_25595; -.
KEGG; msg:MSMEI_5041; -.
KEGG; msm:MSMEG_5175; -.
PATRIC; fig|246196.19.peg.5049; -.
eggNOG; ENOG4105NDF; Bacteria.
eggNOG; COG0846; LUCA.
HOGENOM; HOG000085950; -.
KO; K12410; -.
OMA; SMQVYPA; -.
OrthoDB; POG091H02GG; -.
Proteomes; UP000000757; Chromosome.
Proteomes; UP000006158; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0070403; F:NAD+ binding; IEA:UniProtKB-UniRule.
GO; GO:0034979; F:NAD-dependent protein deacetylase activity; IEA:UniProtKB-UniRule.
GO; GO:0036054; F:protein-malonyllysine demalonylase activity; IEA:InterPro.
GO; GO:0036055; F:protein-succinyllysine desuccinylase activity; IEA:UniProtKB-UniRule.
GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
GO; GO:0071479; P:cellular response to ionizing radiation; IMP:UniProtKB.
GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IMP:UniProtKB.
CDD; cd01412; SIRT5_Af1_CobB; 1.
Gene3D; 3.30.1600.10; -; 2.
HAMAP; MF_01121; Sirtuin_ClassIII; 1.
InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
InterPro; IPR003000; Sirtuin.
InterPro; IPR026591; Sirtuin_cat_small_dom_sf.
InterPro; IPR027546; Sirtuin_class_III.
InterPro; IPR026590; Ssirtuin_cat_dom.
Pfam; PF02146; SIR2; 1.
SUPFAM; SSF52467; SSF52467; 1.
PROSITE; PS50305; SIRTUIN; 1.
1: Evidence at protein level;
Complete proteome; Cytoplasm; Direct protein sequencing; DNA damage;
DNA repair; Hydrolase; Metal-binding; NAD; Reference proteome; Zinc.
CHAIN 1 240 NAD-dependent protein deacylase Sir2.
/FTId=PRO_0000425954.
DOMAIN 1 240 Deacetylase sirtuin-type.
{ECO:0000255|HAMAP-Rule:MF_01121}.
NP_BIND 8 28 NAD. {ECO:0000255|HAMAP-Rule:MF_01121}.
NP_BIND 86 89 NAD. {ECO:0000255|HAMAP-Rule:MF_01121}.
NP_BIND 177 179 NAD. {ECO:0000255|HAMAP-Rule:MF_01121}.
NP_BIND 203 205 NAD. {ECO:0000255|HAMAP-Rule:MF_01121}.
ACT_SITE 104 104 Proton acceptor. {ECO:0000255|HAMAP-
Rule:MF_01121}.
METAL 112 112 Zinc. {ECO:0000255|HAMAP-Rule:MF_01121}.
METAL 115 115 Zinc. {ECO:0000255|HAMAP-Rule:MF_01121}.
METAL 138 138 Zinc. {ECO:0000255|HAMAP-Rule:MF_01121}.
METAL 140 140 Zinc. {ECO:0000255|HAMAP-Rule:MF_01121}.
BINDING 53 53 Substrate. {ECO:0000255|HAMAP-
Rule:MF_01121}.
BINDING 56 56 Substrate. {ECO:0000255|HAMAP-
Rule:MF_01121}.
BINDING 221 221 NAD; via amide nitrogen.
{ECO:0000255|HAMAP-Rule:MF_01121}.
SEQUENCE 240 AA; 26126 MW; 7CE740A9C5FDE76F CRC64;
MQVTVLSGAG ISAESGVPTF RDAETGLWAQ VDPYEISSTD GWQRNPEKVW AWYLWRHYMM
ARVAPNEAHR TVAAWEDHLD VRVVTQNIDD LHERAGSTNV YHLHGSLFEF RCDACGSAFE
GNLPEMPEPV ETIDPPVCPC SGLIRPSVVW FGEPLPDAAW NRSVLAVSSA DVVIVVGTSS
IVYPAAGLPE AALAAGKPVI EVNPERTPLS DSATVSLRET ASEALPTLLQ RLPELLNRSA


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