DEACT_AGRFC
ID DEACT_AGRFC Reviewed; 407 AA.
AC Q7CS13;
DT 14-MAY-2014, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 2.
DT 03-AUG-2022, entry version 92.
DE RecName: Full=Deacetylase Atu3266;
DE EC=3.1.1.-;
GN OrderedLocusNames=Atu3266;
OS Agrobacterium fabrum (strain C58 / ATCC 33970) (Agrobacterium tumefaciens
OS (strain C58)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium;
OC Agrobacterium tumefaciens complex.
OX NCBI_TaxID=176299;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743193; DOI=10.1126/science.1066804;
RA Wood D.W., Setubal J.C., Kaul R., Monks D.E., Kitajima J.P., Okura V.K.,
RA Zhou Y., Chen L., Wood G.E., Almeida N.F. Jr., Woo L., Chen Y.,
RA Paulsen I.T., Eisen J.A., Karp P.D., Bovee D. Sr., Chapman P.,
RA Clendenning J., Deatherage G., Gillet W., Grant C., Kutyavin T., Levy R.,
RA Li M.-J., McClelland E., Palmieri A., Raymond C., Rouse G.,
RA Saenphimmachak C., Wu Z., Romero P., Gordon D., Zhang S., Yoo H., Tao Y.,
RA Biddle P., Jung M., Krespan W., Perry M., Gordon-Kamm B., Liao L., Kim S.,
RA Hendrick C., Zhao Z.-Y., Dolan M., Chumley F., Tingey S.V., Tomb J.-F.,
RA Gordon M.P., Olson M.V., Nester E.W.;
RT "The genome of the natural genetic engineer Agrobacterium tumefaciens
RT C58.";
RL Science 294:2317-2323(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C58 / ATCC 33970;
RX PubMed=11743194; DOI=10.1126/science.1066803;
RA Goodner B., Hinkle G., Gattung S., Miller N., Blanchard M., Qurollo B.,
RA Goldman B.S., Cao Y., Askenazi M., Halling C., Mullin L., Houmiel K.,
RA Gordon J., Vaudin M., Iartchouk O., Epp A., Liu F., Wollam C., Allinger M.,
RA Doughty D., Scott C., Lappas C., Markelz B., Flanagan C., Crowell C.,
RA Gurson J., Lomo C., Sear C., Strub G., Cielo C., Slater S.;
RT "Genome sequence of the plant pathogen and biotechnology agent
RT Agrobacterium tumefaciens C58.";
RL Science 294:2323-2328(2001).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.62 ANGSTROMS) IN COMPLEX WITH ZINC, CARBOXYLATION
RP AT LYS-173, COFACTOR, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND
RP LACK OF DIHYDROOROTASE ACTIVITY.
RC STRAIN=C58 / ATCC 33970;
RX PubMed=23214420; DOI=10.1021/bi301483z;
RA Ornelas A., Korczynska M., Ragumani S., Kumaran D., Narindoshvili T.,
RA Shoichet B.K., Swaminathan S., Raushel F.M.;
RT "Functional annotation and three-dimensional structure of an incorrectly
RT annotated dihydroorotase from cog3964 in the amidohydrolase superfamily.";
RL Biochemistry 52:228-238(2013).
CC -!- FUNCTION: Esterase that catalyzes the deacetylation of acetyl-(R)-
CC mandelate (in vitro). Can also hydrolyze acetyl glycolate, but with
CC lower efficiency. Has very low N-acetyl-D-amino acid deacetylase
CC activity with N-acetyl-D-serine and N-acetyl-D-threonine (in vitro).
CC Theoretical substrate docking studies suggest that other N-acetylated
CC amino acids may optimally occupy the active site and may in fact be the
CC physiological substrates. {ECO:0000269|PubMed:23214420}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:23214420};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000269|PubMed:23214420};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.0 mM for acetyl-(R)-mandelate {ECO:0000269|PubMed:23214420};
CC -!- SUBUNIT: Homohexamer, dimer of trimers. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC Atu3266/EF_0837 deacetylase family. {ECO:0000305}.
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DR EMBL; AE007870; AAK90124.2; -; Genomic_DNA.
DR RefSeq; NP_357339.2; NC_003063.2.
DR RefSeq; WP_010972896.1; NC_003063.2.
DR PDB; 2OGJ; X-ray; 2.62 A; A/B/C/D/E/F=2-407.
DR PDBsum; 2OGJ; -.
DR AlphaFoldDB; Q7CS13; -.
DR SMR; Q7CS13; -.
DR STRING; 176299.Atu3266; -.
DR EnsemblBacteria; AAK90124; AAK90124; Atu3266.
DR GeneID; 66223577; -.
DR KEGG; atu:Atu3266; -.
DR PATRIC; fig|176299.10.peg.3108; -.
DR eggNOG; COG3964; Bacteria.
DR HOGENOM; CLU_036699_2_0_5; -.
DR OMA; IGNNPPN; -.
DR PhylomeDB; Q7CS13; -.
DR BioCyc; AGRO:ATU3266-MON; -.
DR EvolutionaryTrace; Q7CS13; -.
DR Proteomes; UP000000813; Chromosome linear.
DR GO; GO:0019213; F:deacetylase activity; IEA:InterPro.
DR GO; GO:0016810; F:hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR Gene3D; 2.30.40.10; -; 1.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR020043; Deacetylase_Atu3266-like.
DR InterPro; IPR011059; Metal-dep_hydrolase_composite.
DR InterPro; IPR032466; Metal_Hydrolase.
DR PANTHER; PTHR42717; PTHR42717; 1.
DR Pfam; PF01979; Amidohydro_1; 1.
DR PIRSF; PIRSF039004; ADE_EF_0837; 1.
DR SUPFAM; SSF51338; SSF51338; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Hydrolase; Metal-binding; Reference proteome; Zinc.
FT CHAIN 1..407
FT /note="Deacetylase Atu3266"
FT /id="PRO_0000429019"
FT BINDING 75
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:23214420"
FT BINDING 77
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:23214420"
FT BINDING 173
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:23214420"
FT BINDING 173
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /note="via carbamate group"
FT /evidence="ECO:0000269|PubMed:23214420"
FT BINDING 206
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:23214420"
FT BINDING 229
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000269|PubMed:23214420"
FT BINDING 289
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000269|PubMed:23214420"
FT SITE 175
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000305"
FT MOD_RES 173
FT /note="N6-carboxylysine"
FT /evidence="ECO:0000269|PubMed:23214420"
FT STRAND 15..22
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 34..38
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 42..48
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 57..59
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 66..69
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 71..76
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 94..96
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 98..106
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 112..118
FT /evidence="ECO:0007829|PDB:2OGJ"
FT TURN 119..122
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 124..134
FT /evidence="ECO:0007829|PDB:2OGJ"
FT TURN 135..143
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 150..152
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 155..163
FT /evidence="ECO:0007829|PDB:2OGJ"
FT TURN 166..168
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 169..177
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 178..181
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 187..199
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 203..207
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 209..212
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 214..220
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 226..228
FT /evidence="ECO:0007829|PDB:2OGJ"
FT TURN 229..231
FT /evidence="ECO:0007829|PDB:2OGJ"
FT TURN 235..237
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 243..251
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 258..260
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 265..267
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 270..278
FT /evidence="ECO:0007829|PDB:2OGJ"
FT TURN 292..298
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 302..311
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 316..321
FT /evidence="ECO:0007829|PDB:2OGJ"
FT TURN 322..324
FT /evidence="ECO:0007829|PDB:2OGJ"
FT HELIX 325..330
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 346..360
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 366..380
FT /evidence="ECO:0007829|PDB:2OGJ"
FT STRAND 383..386
FT /evidence="ECO:0007829|PDB:2OGJ"
SQ SEQUENCE 407 AA; 43969 MW; 4918E8F71435125A CRC64;
MTSGEQAKTP LQAPILLTNV KPVGFGKGAS QSSTDILIGG DGKIAAVGSA LQAPADTQRI
DAKGAFISPG WVDLHVHIWH GGTDISIRPS ECGAERGVTT LVDAGSAGEA NFHGFREYII
EPSRERIKAF LNLGSIGLVA CNRVPELRDI KDIDLDRILE CYAENSEHIV GLKVRASHVI
TGSWGVTPVK LGKKIAKILK VPMMVHVGEP PALYDEVLEI LGPGDVVTHC FNGKSGSSIM
EDEDLFNLAE RCAGEGIRLD IGHGGASFSF KVAEAAIARG LLPFSISTDL HGHSMNFPVW
DLATTMSKLL SVDMPFENVV EAVTRNPASV IRLDMENRLD VGQRADFTVF DLVDADLEAT
DSNGDVSRLK RLFEPRYAVI GAEAIAASRY IPRARKLVRH SHGYSWR
