DPES_AGRFC
ID DPES_AGRFC Reviewed; 289 AA.
AC A9CH28;
DT 17-FEB-2016, integrated into UniProtKB/Swiss-Prot.
DT 15-JAN-2008, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=D-psicose 3-epimerase {ECO:0000303|PubMed:16461638};
DE Short=DPEase {ECO:0000303|PubMed:16461638};
DE EC=5.1.3.30 {ECO:0000269|PubMed:16461638};
GN Name=dpe; OrderedLocusNames=Atu4750;
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 FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ACTIVITY
RP REGULATION, SUBSTRATE SPECIFICITY, COFACTOR, AND SUBUNIT.
RX PubMed=16461638; DOI=10.1128/aem.72.2.981-985.2006;
RA Kim H.J., Hyun E.K., Kim Y.S., Lee Y.J., Oh D.K.;
RT "Characterization of an Agrobacterium tumefaciens D-psicose 3-epimerase
RT that converts D-fructose to D-psicose.";
RL Appl. Environ. Microbiol. 72:981-985(2006).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOG AND
RP MANGANESE ION, COFACTOR, AND SUBUNIT.
RX PubMed=16876192; DOI=10.1016/j.jmb.2006.06.069;
RA Kim K., Kim H.J., Oh D.K., Cha S.S., Rhee S.;
RT "Crystal structure of D-psicose 3-epimerase from Agrobacterium tumefaciens
RT and its complex with true substrate D-fructose: a pivotal role of metal in
RT catalysis, an active site for the non-phosphorylated substrate, and its
RT conformational changes.";
RL J. Mol. Biol. 361:920-931(2006).
CC -!- FUNCTION: Involved in the biosynthesis of D-psicose. Catalyzes the
CC reversible epimerization of D-fructose at the C3 position to yield D-
CC psicose. The enzyme is highly specific for D-psicose and shows very low
CC activity with D-tagatose. The substrate specificity decreases in the
CC following order: D-fructose, D-tagatose, D-ribulose, D-xylulose, and D-
CC sorbose. It shows a higher level of activity for cis ketoses than for
CC trans-ketoses. {ECO:0000269|PubMed:16461638}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-allulose = keto-D-fructose; Xref=Rhea:RHEA:42360,
CC ChEBI:CHEBI:27605, ChEBI:CHEBI:48095; EC=5.1.3.30;
CC Evidence={ECO:0000269|PubMed:16461638};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000269|PubMed:16461638, ECO:0000269|PubMed:16876192};
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000269|PubMed:16461638};
CC Note=Binds 1 Mn(2+) or Co(2+) ion per subunit.
CC {ECO:0000269|PubMed:16461638, ECO:0000269|PubMed:16876192};
CC -!- ACTIVITY REGULATION: Inhibited by Zn(2+) and Cu(2+).
CC {ECO:0000269|PubMed:16461638}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=12 mM for D-psicose (at pH 8 and 50 degrees Celsius)
CC {ECO:0000269|PubMed:16461638};
CC KM=762 mM for D-tagatose (at pH 8 and 50 degrees Celsius)
CC {ECO:0000269|PubMed:16461638};
CC Note=kcat is 2381 min(-1) for epimerase activity with D-psicose as
CC substrate (at pH 8 and 50 degrees Celsius). kcat is 270 min(-1) for
CC epimerase activity with D-tagatose as substrate (at pH 8 and 50
CC degrees Celsius). {ECO:0000269|PubMed:16461638};
CC pH dependence:
CC Optimum pH is 8. {ECO:0000269|PubMed:16461638};
CC Temperature dependence:
CC Optimum temperature is 50 degrees Celsius. The activity of D-psicose
CC 3-epimerase is very stable below 45 degrees Celsius but decreases
CC above 50 degrees Celsius with increasing reaction time.
CC {ECO:0000269|PubMed:16461638};
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:16461638,
CC ECO:0000269|PubMed:16876192}.
CC -!- SIMILARITY: Belongs to the hyi family. {ECO:0000305}.
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DR EMBL; AE007870; AAK88700.1; -; Genomic_DNA.
DR PIR; AB3141; AB3141.
DR PIR; B98147; B98147.
DR RefSeq; NP_355915.1; NC_003063.2.
DR RefSeq; WP_010974125.1; NC_003063.2.
DR PDB; 2HK0; X-ray; 2.00 A; A/B/C/D=1-289.
DR PDB; 2HK1; X-ray; 2.30 A; A/B/C/D=1-289.
DR PDBsum; 2HK0; -.
DR PDBsum; 2HK1; -.
DR AlphaFoldDB; A9CH28; -.
DR SMR; A9CH28; -.
DR STRING; 176299.Atu4750; -.
DR EnsemblBacteria; AAK88700; AAK88700; Atu4750.
DR KEGG; atu:Atu4750; -.
DR PATRIC; fig|176299.10.peg.4557; -.
DR eggNOG; COG1082; Bacteria.
DR HOGENOM; CLU_050006_8_2_5; -.
DR OMA; NMALAKH; -.
DR PhylomeDB; A9CH28; -.
DR BioCyc; AGRO:ATU4750-MON; -.
DR BioCyc; MetaCyc:MON-17958; -.
DR BRENDA; 5.1.3.B12; 200.
DR EvolutionaryTrace; A9CH28; -.
DR Proteomes; UP000000813; Chromosome linear.
DR GO; GO:0050897; F:cobalt ion binding; IDA:UniProtKB.
DR GO; GO:0030145; F:manganese ion binding; IDA:UniProtKB.
DR GO; GO:0016857; F:racemase and epimerase activity, acting on carbohydrates and derivatives; IDA:UniProtKB.
DR InterPro; IPR036237; Xyl_isomerase-like_sf.
DR InterPro; IPR013022; Xyl_isomerase-like_TIM-brl.
DR Pfam; PF01261; AP_endonuc_2; 1.
DR SUPFAM; SSF51658; SSF51658; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cobalt; Isomerase; Manganese; Metal-binding;
KW Reference proteome.
FT CHAIN 1..289
FT /note="D-psicose 3-epimerase"
FT /id="PRO_0000435451"
FT ACT_SITE 150
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT ACT_SITE 244
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q9WYP7"
FT BINDING 6
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:B8I944"
FT BINDING 107
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16876192"
FT BINDING 150
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:16876192"
FT BINDING 156
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16876192"
FT BINDING 183..186
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16876192"
FT BINDING 183
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:16876192"
FT BINDING 209
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:16876192"
FT BINDING 215
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:16876192"
FT BINDING 244
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /evidence="ECO:0000269|PubMed:16876192"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 7..10
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 21..27
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 31..36
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 37..40
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 45..57
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 61..65
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 70..72
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 79..98
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 103..106
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 122..142
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 146..150
FT /evidence="ECO:0007829|PDB:2HK0"
FT TURN 154..156
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 163..173
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 178..183
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 184..190
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 194..201
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 202..204
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 205..210
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 225..234
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 239..243
FT /evidence="ECO:0007829|PDB:2HK0"
FT HELIX 251..256
FT /evidence="ECO:0007829|PDB:2HK0"
FT STRAND 264..266
FT /evidence="ECO:0007829|PDB:2HK1"
FT HELIX 269..287
FT /evidence="ECO:0007829|PDB:2HK0"
SQ SEQUENCE 289 AA; 31566 MW; 4656232075FE1A19 CRC64;
MKHGIYYSYW EHEWSAKFGP YIEKVAKLGF DIIEVAAHHI NEYSDAELAT IRKSAKDNGI
ILTAGIGPSK TKNLSSEDAA VRAAGKAFFE RTLSNVAKLD IHTIGGALHS YWPIDYSQPV
DKAGDYARGV EGINGIADFA NDLGINLCIE VLNRFENHVL NTAAEGVAFV KDVGKNNVKV
MLDTFHMNIE EDSFGDAIRT AGPLLGHFHT GESNRRVPGK GRMPWHEIGL ALRDINYTGA
VIMEPFVKTG GTIGSDIKVW RDLSGGADIA KMDEDARNAL AFSRFVLGG
