NPD_YERPS
ID NPD_YERPS Reviewed; 278 AA.
AC Q669P6;
DT 15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 07-SEP-2016, sequence version 3.
DT 03-AUG-2022, entry version 100.
DE RecName: Full=NAD-dependent protein deacylase {ECO:0000255|HAMAP-Rule:MF_01121};
DE EC=2.3.1.286 {ECO:0000255|HAMAP-Rule:MF_01121};
DE AltName: Full=Regulatory protein SIR2 homolog {ECO:0000255|HAMAP-Rule:MF_01121};
GN Name=cobB {ECO:0000255|HAMAP-Rule:MF_01121}; OrderedLocusNames=YPTB2438;
OS Yersinia pseudotuberculosis serotype I (strain IP32953).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=273123;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IP32953;
RX PubMed=15358858; DOI=10.1073/pnas.0404012101;
RA Chain P.S.G., Carniel E., Larimer F.W., Lamerdin J., Stoutland P.O.,
RA Regala W.M., Georgescu A.M., Vergez L.M., Land M.L., Motin V.L.,
RA Brubaker R.R., Fowler J., Hinnebusch J., Marceau M., Medigue C.,
RA Simonet M., Chenal-Francisque V., Souza B., Dacheux D., Elliott J.M.,
RA Derbise A., Hauser L.J., Garcia E.;
RT "Insights into the evolution of Yersinia pestis through whole-genome
RT comparison with Yersinia pseudotuberculosis.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:13826-13831(2004).
CC -!- FUNCTION: NAD-dependent lysine deacetylase that specifically removes
CC acetyl groups on target proteins. Also acts as a protein-lysine
CC deacylase by mediating protein desuccinylation and de-2-
CC hydroxyisobutyrylation. Modulates the activities of several proteins
CC which are inactive in their acylated form. {ECO:0000255|HAMAP-
CC Rule:MF_01121}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-acetyl-L-lysyl-[protein] + NAD(+) = 2''-O-acetyl-
CC ADP-D-ribose + L-lysyl-[protein] + nicotinamide;
CC Xref=Rhea:RHEA:43636, Rhea:RHEA-COMP:9752, Rhea:RHEA-COMP:10731,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:17154, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:61930, ChEBI:CHEBI:83767;
CC EC=2.3.1.286; Evidence={ECO:0000255|HAMAP-Rule:MF_01121};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-succinyl-L-lysyl-[protein] + NAD(+) = 2''-O-
CC succinyl-ADP-D-ribose + L-lysyl-[protein] + nicotinamide;
CC Xref=Rhea:RHEA:47668, Rhea:RHEA-COMP:9752, Rhea:RHEA-COMP:11877,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:17154, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:87830, ChEBI:CHEBI:87832;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01121};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N(6)-(2-hydroxyisobutanoyl)-L-lysyl-[protein] + NAD(+) =
CC 2''-O-(2-hydroxyisobutanoyl)-ADP-D-ribose + L-lysyl-[protein] +
CC nicotinamide; Xref=Rhea:RHEA:24364, Rhea:RHEA-COMP:9752, Rhea:RHEA-
CC COMP:15921, ChEBI:CHEBI:15377, ChEBI:CHEBI:17154, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:57540, ChEBI:CHEBI:144968, ChEBI:CHEBI:144969;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01121};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01121};
CC Note=Binds 1 zinc ion per subunit. {ECO:0000255|HAMAP-Rule:MF_01121};
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01121}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative promoter usage; Named isoforms=2;
CC Name=CobB-Long {ECO:0000250|UniProtKB:P0A2F2};
CC IsoId=Q669P6-1; Sequence=Displayed;
CC Name=CobB-Short {ECO:0000250|UniProtKB:P0A2F2};
CC IsoId=Q669P6-2; Sequence=VSP_058465;
CC -!- DOMAIN: 2 residues (Tyr-90 and Arg-93) present in a large hydrophobic
CC pocket are probably involved in substrate specificity. They are
CC important for desuccinylation activity, but dispensable for
CC deacetylation activity. {ECO:0000255|HAMAP-Rule:MF_01121}.
CC -!- SIMILARITY: Belongs to the sirtuin family. Class III subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01121}.
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DR EMBL; BX936398; CAH21676.1; -; Genomic_DNA.
DR RefSeq; WP_002210921.1; NZ_CP009712.1.
DR AlphaFoldDB; Q669P6; -.
DR SMR; Q669P6; -.
DR PRIDE; Q669P6; -.
DR EnsemblBacteria; CAH21676; CAH21676; YPTB2438.
DR GeneID; 66841131; -.
DR KEGG; ypo:BZ17_12; -.
DR KEGG; yps:YPTB2438; -.
DR PATRIC; fig|273123.14.peg.13; -.
DR OMA; SMQVYPA; -.
DR Proteomes; UP000001011; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0070403; F:NAD+ binding; IEA:UniProtKB-UniRule.
DR GO; GO:0160013; F:NAD-dependent protein de-2-hydroxyisobutyrylase activity; IEA:RHEA.
DR GO; GO:0034979; F:NAD-dependent protein deacetylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0036054; F:protein-malonyllysine demalonylase activity; IEA:InterPro.
DR GO; GO:0036055; F:protein-succinyllysine desuccinylase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006476; P:protein deacetylation; IEA:UniProtKB-UniRule.
DR CDD; cd01412; SIRT5_Af1_CobB; 1.
DR Gene3D; 3.30.1600.10; -; 1.
DR HAMAP; MF_01121; Sirtuin_ClassIII; 1.
DR InterPro; IPR029035; DHS-like_NAD/FAD-binding_dom.
DR InterPro; IPR003000; Sirtuin.
DR InterPro; IPR026591; Sirtuin_cat_small_dom_sf.
DR InterPro; IPR027546; Sirtuin_class_III.
DR InterPro; IPR026590; Ssirtuin_cat_dom.
DR Pfam; PF02146; SIR2; 1.
DR SUPFAM; SSF52467; SSF52467; 1.
DR PROSITE; PS50305; SIRTUIN; 1.
PE 3: Inferred from homology;
KW Alternative promoter usage; Cytoplasm; Metal-binding; NAD; Transferase;
KW Zinc.
FT CHAIN 1..278
FT /note="NAD-dependent protein deacylase"
FT /id="PRO_0000110375"
FT DOMAIN 1..272
FT /note="Deacetylase sirtuin-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT ACT_SITE 145
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 46..65
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 90
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 93
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 127..130
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 153
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 172
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 212..214
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 238..240
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT BINDING 256
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT VAR_SEQ 1..35
FT /note="Missing (in isoform CobB-Short)"
FT /evidence="ECO:0000250|UniProtKB:P0A2F2"
FT /id="VSP_058465"
SQ SEQUENCE 278 AA; 31845 MW; E134527A872AB8DB CRC64;
MRIRHRLCRF RKSKHVRHQR FRSRIFHRDS AVAKEMKKPF VVVLTGAGIS AESGIRTFRA
DDGLWEDHRV EDVATPEGYR RDPELVQRFY NERRRQLQQP DIAPNAAHFA LADLEAVLGD
NLVLITQNID NLHERAGSKR VIHMHGELLK VRCTQSGQVL DWQGDLSADE RCHCCQFPSP
LRPHIVWFGE MPMGMDDIYQ ALAEADFFIS IGTSGHVYPA AGFVHESHLH GAHTVELNLE
PSQVESQFDE KHYGLASKVV PEYIREFLTT CGENRQGD
