4HYPE_PARDP
ID 4HYPE_PARDP Reviewed; 334 AA.
AC A1BBM5;
DT 19-FEB-2014, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 80.
DE RecName: Full=4-hydroxyproline 2-epimerase {ECO:0000303|PubMed:24056934, ECO:0000303|PubMed:24980702};
DE Short=4Hyp 2-epimerase {ECO:0000303|PubMed:24056934};
DE Short=4HypE {ECO:0000303|PubMed:24980702};
DE EC=5.1.1.8 {ECO:0000269|PubMed:24056934, ECO:0000269|PubMed:24980702};
GN Name=hypF; OrderedLocusNames=Pden_4859;
OS Paracoccus denitrificans (strain Pd 1222).
OG Plasmid pPD1222.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Paracoccus.
OX NCBI_TaxID=318586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Pd 1222;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S.,
RA Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M.,
RA Richardson P.;
RT "Complete sequence of plasmid 1 of Paracoccus denitrificans PD1222.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, GENE NAME, DISRUPTION
RP PHENOTYPE, AND PATHWAY.
RC STRAIN=Pd 1222;
RX PubMed=24056934; DOI=10.1038/nature12576;
RA Zhao S., Kumar R., Sakai A., Vetting M.W., Wood B.M., Brown S.,
RA Bonanno J.B., Hillerich B.S., Seidel R.D., Babbitt P.C., Almo S.C.,
RA Sweedler J.V., Gerlt J.A., Cronan J.E., Jacobson M.P.;
RT "Discovery of new enzymes and metabolic pathways by using structure and
RT genome context.";
RL Nature 502:698-702(2013).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND INDUCTION.
RX PubMed=24980702; DOI=10.7554/elife.03275;
RA Zhao S., Sakai A., Zhang X., Vetting M.W., Kumar R., Hillerich B.,
RA San Francisco B., Solbiati J., Steves A., Brown S., Akiva E., Barber A.,
RA Seidel R.D., Babbitt P.C., Almo S.C., Gerlt J.A., Jacobson M.P.;
RT "Prediction and characterization of enzymatic activities guided by sequence
RT similarity and genome neighborhood networks.";
RL Elife 3:E03275-E03275(2014).
CC -!- FUNCTION: Catalyzes the epimerization of trans-4-hydroxy-L-proline
CC (t4LHyp) to cis-4-hydroxy-D-proline (c4DHyp). Is likely involved in a
CC degradation pathway that converts t4LHyp to alpha-ketoglutarate, which
CC would allow P.denitrificans to grow on t4LHyp as a sole carbon source
CC (PubMed:24980702). Also seems to be involved in an alternative
CC catabolic pathway that degrades trans-4-hydroxy-L-proline betaine
CC (tHyp-B) to alpha-ketoglutarate; this pathway would permit the
CC utilization of tHyp-B as a sole carbon and nitrogen source
CC (PubMed:24056934). {ECO:0000269|PubMed:24056934,
CC ECO:0000269|PubMed:24980702}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=trans-4-hydroxy-L-proline = cis-4-hydroxy-D-proline;
CC Xref=Rhea:RHEA:21152, ChEBI:CHEBI:57690, ChEBI:CHEBI:58375;
CC EC=5.1.1.8; Evidence={ECO:0000269|PubMed:24056934,
CC ECO:0000269|PubMed:24980702};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=24 mM for trans-4-hydroxy-L-proline {ECO:0000269|PubMed:24056934};
CC KM=25 mM for trans-4-hydroxy-L-proline {ECO:0000269|PubMed:24980702};
CC Note=kcat is 15 sec(-1) (PubMed:24056934). kcat is 16 sec(-1)
CC (PubMed:24980702). {ECO:0000269|PubMed:24056934,
CC ECO:0000269|PubMed:24980702};
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- INDUCTION: Is up-regulated when the bacterium is grown on t4LHyp as
CC sole carbon source. {ECO:0000269|PubMed:24980702}.
CC -!- DISRUPTION PHENOTYPE: Cells lacking both hpbD and hypF are unable to
CC utilize tHyp-B or t4LHyp as sole carbon source.
CC {ECO:0000269|PubMed:24056934}.
CC -!- SIMILARITY: Belongs to the proline racemase family. {ECO:0000305}.
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DR EMBL; CP000491; ABL72919.1; -; Genomic_DNA.
DR RefSeq; WP_011751078.1; NC_008688.1.
DR AlphaFoldDB; A1BBM5; -.
DR SMR; A1BBM5; -.
DR STRING; 318586.Pden_4859; -.
DR PRIDE; A1BBM5; -.
DR EnsemblBacteria; ABL72919; ABL72919; Pden_4859.
DR KEGG; pde:Pden_4859; -.
DR eggNOG; COG3938; Bacteria.
DR HOGENOM; CLU_036729_0_0_5; -.
DR OMA; SHVLWTG; -.
DR SABIO-RK; A1BBM5; -.
DR Proteomes; UP000000361; Plasmid pPD1222.
DR GO; GO:0047580; F:4-hydroxyproline epimerase activity; IDA:UniProtKB.
DR GO; GO:0006579; P:amino-acid betaine catabolic process; IMP:UniProtKB.
DR InterPro; IPR008794; Pro_racemase_fam.
DR PANTHER; PTHR33442; PTHR33442; 1.
DR Pfam; PF05544; Pro_racemase; 1.
DR PIRSF; PIRSF029792; Pro_racemase; 1.
DR SFLD; SFLDS00028; Proline_Racemase; 1.
PE 1: Evidence at protein level;
KW Isomerase; Plasmid; Reference proteome.
FT CHAIN 1..334
FT /note="4-hydroxyproline 2-epimerase"
FT /id="PRO_0000425280"
FT ACT_SITE 90
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:Q4KGU2"
FT ACT_SITE 253
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:Q4KGU2"
FT BINDING 91..92
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q4KGU2"
FT BINDING 223
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q4KGU2"
FT BINDING 249
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q4KGU2"
FT BINDING 254..255
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:Q4KGU2"
SQ SEQUENCE 334 AA; 36301 MW; AD1CDA96879701CE CRC64;
MTQYIFPCID GHTCGNPVRL VAGGAPRLEG ATMLEKRAHF LREFDWIRTG LMFEPRGHDM
MSGAILYPPT RGDCDVAVLY IETSGCLPMC GHGTIGTITM GIENGLIVPR TPGRLSIETP
AGKVDIEYRQ EGRHVEEVRL TNVPGFLYAE GLTAEVEGLG EIVVDVAYGG NFYAIVEPQK
NFRDMADHTA GELIGWSLTL RAALNQKYEF THPEHPQING LSHIQWTGAP TVPGAHARNA
VFYGDKAIDR SPCGTGTSAR MAQLAARGRL GVGDEFWHES IIGSIFKGRI EAAATVAGRD
AIIPSIAGWA RQTGLNTIFI DAERDPFAHG FVVK
