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NPD_SALTY
ID   NPD_SALTY               Reviewed;         273 AA.
AC   P0A2F2; P97013;
DT   15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT   07-SEP-2016, sequence version 3.
DT   03-AUG-2022, entry version 99.
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, ECO:0000303|PubMed:8206834};
GN   OrderedLocusNames=STM1221;
OS   Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Salmonella.
OX   NCBI_TaxID=99287;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND DISRUPTION PHENOTYPE.
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=8955330; DOI=10.1128/jb.178.23.7016-7019.1996;
RA   Tsang A.W., Escalante-Semerena J.C.;
RT   "cobB function is required for catabolism of propionate in Salmonella
RT   typhimurium LT2: evidence for existence of a substitute function for CobB
RT   within the 1,2-propanediol utilization (pdu) operon.";
RL   J. Bacteriol. 178:7016-7019(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=11677609; DOI=10.1038/35101614;
RA   McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P.,
RA   Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D.,
RA   Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E.,
RA   Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R.,
RA   Wilson R.K.;
RT   "Complete genome sequence of Salmonella enterica serovar Typhimurium LT2.";
RL   Nature 413:852-856(2001).
RN   [3]
RP   DISRUPTION PHENOTYPE.
RC   STRAIN=LT2;
RX   PubMed=8206834; DOI=10.1128/jb.176.12.3568-3575.1994;
RA   Trzebiatowski J.R., O'Toole G.A., Escalante-Semerena J.C.;
RT   "The cobT gene of Salmonella typhimurium encodes the NaMN: 5,6-
RT   dimethylbenzimidazole phosphoribosyltransferase responsible for the
RT   synthesis of N1-(5-phospho-alpha-D-ribosyl)-5,6-dimethylbenzimidazole, an
RT   intermediate in the synthesis of the nucleotide loop of cobalamin.";
RL   J. Bacteriol. 176:3568-3575(1994).
RN   [4]
RP   FUNCTION.
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=9822644; DOI=10.1074/jbc.273.48.31788;
RA   Tsang A.W., Escalante-Semerena J.C.;
RT   "CobB, a new member of the SIR2 family of eucaryotic regulatory proteins,
RT   is required to compensate for the lack of nicotinate mononucleotide:5,6-
RT   dimethylbenzimidazole phosphoribosyltransferase activity in cobT mutants
RT   during cobalamin biosynthesis in Salmonella typhimurium LT2.";
RL   J. Biol. Chem. 273:31788-31794(1998).
RN   [5]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=12493915; DOI=10.1126/science.1077650;
RA   Starai V.J., Celic I., Cole R.N., Boeke J.D., Escalante-Semerena J.C.;
RT   "Sir2-dependent activation of acetyl-CoA synthetase by deacetylation of
RT   active lysine.";
RL   Science 298:2390-2392(2002).
RN   [6]
RP   FUNCTION AS AN NAD-DEPENDENT DEACETYLASE.
RC   STRAIN=LT2 / SGSC1412 / ATCC 700720;
RX   PubMed=10841563; DOI=10.1073/pnas.97.12.6658;
RA   Smith J.S., Brachmann C.B., Celic I., Kenna M.A., Muhammad S., Starai V.J.,
RA   Avalos J.L., Escalante-Semerena J.C., Grubmeyer C., Wolberger C.,
RA   Boeke J.D.;
RT   "A phylogenetically conserved NAD+-dependent protein deacetylase activity
RT   in the Sir2 protein family.";
RL   Proc. Natl. Acad. Sci. U.S.A. 97:6658-6663(2000).
RN   [7]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=LT2;
RX   PubMed=12700259; DOI=10.1128/jb.185.9.2802-2810.2003;
RA   Palacios S., Starai V.J., Escalante-Semerena J.C.;
RT   "Propionyl coenzyme A is a common intermediate in the 1,2-propanediol and
RT   propionate catabolic pathways needed for expression of the prpBCDE operon
RT   during growth of Salmonella enterica on 1,2-propanediol.";
RL   J. Bacteriol. 185:2802-2810(2003).
RN   [8]
RP   FUNCTION, ALTERNATIVE PROMOTER USAGE (ISOFORMS COBB-LONG AND COBB-SHORT),
RP   SUBUNIT, INDUCTION, AND MUTAGENESIS OF MET-1 AND 37-MET-MET-38.
RC   STRAIN=LT2;
RX   PubMed=20889757; DOI=10.1128/jb.00874-10;
RA   Tucker A.C., Escalante-Semerena J.C.;
RT   "Biologically active isoforms of CobB sirtuin deacetylase in Salmonella
RT   enterica and Erwinia amylovora.";
RL   J. Bacteriol. 192:6200-6208(2010).
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 (By similarity). Activates
CC       the enzyme acetyl-CoA synthetase (acs) by deacetylating 'Lys-609' in
CC       the inactive, acetylated form of the enzyme (PubMed:12493915,
CC       PubMed:20889757, PubMed:12700259). May also modulate the activity of
CC       other propionyl-adenosine monophosphate (AMP)-forming enzymes such as
CC       propionate--CoA ligase (prpE) (PubMed:12493915, PubMed:12700259).
CC       Overexpression compensates for a cobT deletion, suggesting it may have
CC       N(1)-alpha-phosphoribosyltransferase activity; alternatively this
CC       protein may stimulate synthesis of an enzyme with the CobT activity
CC       (PubMed:9822644). {ECO:0000255|HAMAP-Rule:MF_01121,
CC       ECO:0000269|PubMed:10841563, ECO:0000269|PubMed:12493915,
CC       ECO:0000269|PubMed:20889757, ECO:0000269|PubMed:9822644,
CC       ECO:0000305|PubMed:12700259}.
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         ECO:0000269|PubMed:20889757};
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   -!- SUBUNIT: Both isoforms are monomers (PubMed:20889757).
CC       {ECO:0000269|PubMed:20889757}.
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:0000269|PubMed:20889757};
CC         IsoId=P0A2F2-1; Sequence=Displayed;
CC       Name=CobB-Short {ECO:0000269|PubMed:20889757};
CC         IsoId=P0A2F2-2; Sequence=VSP_058462;
CC   -!- INDUCTION: Most expressed in mid- to late-log growth phases (at protein
CC       level) (PubMed:20889757). Has 3 promoters, P1 (upstream of nagK) gives
CC       rise to a nagK-cobB transcript, P2 (within the nagK coding region)
CC       gives rise to a transcript able to generate both CobB isoforms, while
CC       P3 (nucleotide 44 of the long isoform) can only give rise to the CobB-
CC       Short isoform (PubMed:20889757). {ECO:0000269|PubMed:20889757}.
CC   -!- DOMAIN: 2 residues (Tyr-92 and Arg-95) 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   -!- DISRUPTION PHENOTYPE: Single mutant grows on cobinamide (CBI), CBI plus
CC       5,6-dimethylbenzimidazole (DMB) and cobalamin (CBL); double cobB-cobT
CC       deletion mutants do not grow on CBI plus DMB (PubMed:8206834). Single
CC       mutant does not grow on propionate (PubMed:8955330). Acetyl-CoA
CC       synthetase (acs) accumulates in an inactive, acetylated form
CC       (PubMed:12493915). Considerably decreased growth on 1,2-propanediol,
CC       cells do not excrete more propanediol than wild-type (PubMed:12700259).
CC       {ECO:0000269|PubMed:12493915, ECO:0000269|PubMed:12700259,
CC       ECO:0000269|PubMed:8206834, ECO:0000269|PubMed:8955330}.
CC   -!- MISCELLANEOUS: Originally isolated genetically as functioning in
CC       cobalamin biosynthesis and in propionate catabolism (PubMed:8206834,
CC       PubMed:8955330). {ECO:0000305|PubMed:8206834,
CC       ECO:0000305|PubMed:8955330}.
CC   -!- MISCELLANEOUS: [Isoform CobB-Long]: The less prevalent isoform.
CC       {ECO:0000269|PubMed:20889757}.
CC   -!- MISCELLANEOUS: [Isoform CobB-Short]: 5- to 20-fold higher levels of
CC       this protein are seen in rich and minimal media.
CC       {ECO:0000269|PubMed:20889757}.
CC   -!- SIMILARITY: Belongs to the sirtuin family. Class III subfamily.
CC       {ECO:0000255|HAMAP-Rule:MF_01121}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAC78722.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305|PubMed:20889757};
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DR   EMBL; U89687; AAC78722.1; ALT_INIT; Genomic_DNA.
DR   EMBL; AE006468; AAL20150.1; -; Genomic_DNA.
DR   RefSeq; NP_460191.1; NC_003197.2. [P0A2F2-1]
DR   RefSeq; WP_001191856.1; NC_003197.2.
DR   AlphaFoldDB; P0A2F2; -.
DR   SMR; P0A2F2; -.
DR   STRING; 99287.STM1221; -.
DR   PaxDb; P0A2F2; -.
DR   EnsemblBacteria; AAL20150; AAL20150; STM1221.
DR   GeneID; 1252739; -.
DR   KEGG; stm:STM1221; -.
DR   PATRIC; fig|99287.12.peg.1290; -.
DR   HOGENOM; CLU_023643_3_1_6; -.
DR   OMA; SMQVYPA; -.
DR   PhylomeDB; P0A2F2; -.
DR   BioCyc; SENT99287:STM1221-MON; -.
DR   PHI-base; PHI:5572; -.
DR   Proteomes; UP000001014; 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:0061697; F:protein-glutaryllysine deglutarylase activity; IBA:GO_Central.
DR   GO; GO:0036054; F:protein-malonyllysine demalonylase activity; IBA:GO_Central.
DR   GO; GO:0036055; F:protein-succinyllysine desuccinylase activity; IBA:GO_Central.
DR   GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0036047; P:peptidyl-lysine demalonylation; IBA:GO_Central.
DR   GO; GO:0036049; P:peptidyl-lysine desuccinylation; IBA:GO_Central.
DR   GO; GO:0006476; P:protein deacetylation; IEA:UniProtKB-UniRule.
DR   GO; GO:0061698; P:protein deglutarylation; IBA:GO_Central.
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   1: Evidence at protein level;
KW   Alternative promoter usage; Cytoplasm; Metal-binding; NAD;
KW   Reference proteome; Transferase; Zinc.
FT   CHAIN           1..273
FT                   /note="NAD-dependent protein deacylase"
FT                   /id="PRO_0000110348"
FT   DOMAIN          1..273
FT                   /note="Deacetylase sirtuin-type"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   ACT_SITE        147
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         48..67
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         92
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         95
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         129..132
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         155
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         174
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         214..216
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         240..242
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   BINDING         258
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01121"
FT   VAR_SEQ         1..37
FT                   /note="Missing (in isoform CobB-Short)"
FT                   /id="VSP_058462"
FT   MUTAGEN         1
FT                   /note="M->A: Complements a cobB deletion, produces only the
FT                   short isoform. Has deacylation and
FT                   phosphoribosyltransferase activities."
FT                   /evidence="ECO:0000269|PubMed:20889757"
FT   MUTAGEN         37..38
FT                   /note="MM->AA: Complements a cobB deletion, produces only
FT                   the long isoform. Has deacylation and
FT                   phosphoribosyltransferase activities."
FT                   /evidence="ECO:0000269|PubMed:20889757"
FT   CONFLICT        115..123
FT                   /note="KLEEALGDR -> NLKKRLAIA (in Ref. 1; AAC78722)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        145
FT                   /note="H -> Q (in Ref. 1; AAC78722)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        248
FT                   /note="S -> N (in Ref. 1; AAC78722)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   273 AA;  31138 MW;  84DEA78DB7FC403C CRC64;
     MQSRRFHRLS RFRKNKRLLR ERLRQRIFFR DRVVPEMMEN PRVLVLTGAG ISAESGIRTF
     RAADGLWEEH RVEDVATPEG FARNPGLVQT FYNARRQQLQ QPEIQPNAAH LALAKLEEAL
     GDRFLLVTQN IDNLHERAGN RNIIHMHGEL LKVRCSQSGQ ILEWNGDVMP EDKCHCCQFP
     APLRPHVVWF GEMPLGMDEI YMALSMADIF IAIGTSGHVY PAAGFVHEAK LHGAHTVELN
     LEPSQVGSEF EEKHYGPASQ VVPEFVDKFL KGL
 
 
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