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4-hydroxyproline betaine 2-epimerase (Hyp-B 2-epimerase) (EC 5.1.1.-) ((4R)-4-hydroxyproline betaine 2-epimerase)

 HPBD_PARDP              Reviewed;         369 AA.
A1B198;
19-FEB-2014, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 1.
12-SEP-2018, entry version 70.
RecName: Full=4-hydroxyproline betaine 2-epimerase;
Short=Hyp-B 2-epimerase;
EC=5.1.1.22 {ECO:0000269|PubMed:24056934, ECO:0000269|PubMed:24520058};
AltName: Full=(4R)-4-hydroxyproline betaine 2-epimerase;
Name=hpbD; OrderedLocusNames=Pden_1187;
Paracoccus denitrificans (strain Pd 1222).
Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
Rhodobacteraceae; Paracoccus.
NCBI_TaxID=318586;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=Pd 1222;
Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H.,
Pitluck S., Munk A.C., Brettin T., Bruce D., Han C., Tapia R.,
Gilna P., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
Lykidis A., Spiro S., Richardson D.J., Moir J.W.B., Ferguson S.J.,
van Spanning R.J.M., Richardson P.;
"Complete sequence of chromosome 1 of Paracoccus denitrificans
PD1222.";
Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
[2]
FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS, GENE NAME,
INDUCTION, DISRUPTION PHENOTYPE, AND PATHWAY.
STRAIN=Pd 1222;
PubMed=24056934; DOI=10.1038/nature12576;
Zhao S., Kumar R., Sakai A., Vetting M.W., Wood B.M., Brown S.,
Bonanno J.B., Hillerich B.S., Seidel R.D., Babbitt P.C., Almo S.C.,
Sweedler J.V., Gerlt J.A., Cronan J.E., Jacobson M.P.;
"Discovery of new enzymes and metabolic pathways by using structure
and genome context.";
Nature 502:698-702(2013).
[3]
X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND
HYDROXYPROLINE BETAINE OR PROLINE BETAINE, COFACTOR, CATALYTIC
ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
PubMed=24520058; DOI=10.1128/mBio.00933-13;
Kumar R., Zhao S., Vetting M.W., Wood B.M., Sakai A., Cho K.,
Solbiati J., Almo S.C., Sweedler J.V., Jacobson M.P., Gerlt J.A.,
Cronan J.E.;
"Prediction and biochemical demonstration of a catabolic pathway for
the osmoprotectant proline betaine.";
MBio 5:E00933-E00933(2014).
-!- FUNCTION: Catalyzes the 2-epimerization of trans-4-hydroxy-L-
proline betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-
B). Is involved in a catabolic pathway that degrades tHyp-B to
alpha-ketoglutarate. This pathway would permit the utilization of
tHyp-B as a carbon and nitrogen source in the absence of osmotic
stress, since tHyp-B functions as an osmolyte and is not
catabolized when it is needed as osmoprotectant. Can also catalyze
the racemization of L-proline betaine.
{ECO:0000269|PubMed:24056934}.
-!- CATALYTIC ACTIVITY: Trans-4-hydroxy-L-proline betaine = cis-4-
hydroxy-D-proline betaine. {ECO:0000269|PubMed:24056934,
ECO:0000269|PubMed:24520058}.
-!- CATALYTIC ACTIVITY: L-proline betaine = D-proline betaine.
{ECO:0000269|PubMed:24056934, ECO:0000269|PubMed:24520058}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:24520058};
Note=Binds 1 Mg(2+) ion per subunit.
{ECO:0000269|PubMed:24520058};
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=64 mM for trans-4-hydroxy-L-proline betaine
{ECO:0000269|PubMed:24056934};
KM=34 mM for L-proline betaine {ECO:0000269|PubMed:24056934};
KM=7.3 mM for D-proline betaine {ECO:0000269|PubMed:24520058};
Note=kcat is 110 sec(-1) with trans-4-hydroxy-L-proline betaine
as substrate (PubMed:24056934). kcat is 68 sec(-1) with L-
proline betaine as substrate (PubMed:24056934). kcat is 28 sec(-
1) with D-proline betaine as substrate (PubMed:24520058).
{ECO:0000269|PubMed:24056934, ECO:0000269|PubMed:24520058};
-!- INDUCTION: Up-regulated by tHyp-B and cHyp-B. Repressed by high
salt concentration. {ECO:0000269|PubMed:24056934}.
-!- DISRUPTION PHENOTYPE: Cells lacking this gene grow more slowly
than wild-type on tHyp-B as sole carbon source, whereas growth is
normal on cHyp-B. When both hpbD and hypF are disrupted,
P.denitrificans is unable to utilize tHyp-B or tHyp as sole carbon
source. {ECO:0000269|PubMed:24056934}.
-!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
enzyme family. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; CP000489; ABL69292.1; -; Genomic_DNA.
RefSeq; WP_011747512.1; NC_008686.1.
PDB; 4E8G; X-ray; 2.00 A; A/B=2-369.
PDB; 4IZG; X-ray; 1.70 A; A/B=1-369.
PDB; 4J1O; X-ray; 1.60 A; A/B=1-369.
PDBsum; 4E8G; -.
PDBsum; 4IZG; -.
PDBsum; 4J1O; -.
ProteinModelPortal; A1B198; -.
SMR; A1B198; -.
STRING; 318586.Pden_1187; -.
PRIDE; A1B198; -.
EnsemblBacteria; ABL69292; ABL69292; Pden_1187.
KEGG; pde:Pden_1187; -.
eggNOG; ENOG4107WEA; Bacteria.
eggNOG; ENOG41107K3; LUCA.
HOGENOM; HOG000140215; -.
KO; K21617; -.
OMA; CTHIGAT; -.
OrthoDB; POG091H04PO; -.
BioCyc; MetaCyc:MONOMER-18941; -.
BioCyc; PDEN318586:G1GW1-1193-MONOMER; -.
Proteomes; UP000000361; Chromosome 1.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0036361; F:racemase activity, acting on amino acids and derivatives; IDA:UniProtKB.
GO; GO:0016855; F:racemase and epimerase activity, acting on amino acids and derivatives; IDA:CACAO.
GO; GO:0006579; P:amino-acid betaine catabolic process; IMP:UniProtKB.
Gene3D; 3.20.20.120; -; 1.
Gene3D; 3.30.390.10; -; 2.
InterPro; IPR034622; 4R-hPro_betaine_2-epimerase.
InterPro; IPR036849; Enolase-like_C_sf.
InterPro; IPR029017; Enolase-like_N.
InterPro; IPR034390; Enolase-like_superfamily.
InterPro; IPR029065; Enolase_C-like.
InterPro; IPR013342; Mandelate_racemase_C.
InterPro; IPR013341; Mandelate_racemase_N_dom.
Pfam; PF13378; MR_MLE_C; 1.
Pfam; PF02746; MR_MLE_N; 1.
SFLD; SFLDF00556; 4R-hydroxyproline_betaine_2-ep; 1.
SFLD; SFLDS00001; Enolase; 1.
SMART; SM00922; MR_MLE; 1.
SUPFAM; SSF51604; SSF51604; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Isomerase; Magnesium; Metal-binding.
CHAIN 1 369 4-hydroxyproline betaine 2-epimerase.
/FTId=PRO_0000425279.
ACT_SITE 164 164 Proton donor/acceptor. {ECO:0000250}.
ACT_SITE 266 266 Proton donor/acceptor. {ECO:0000250}.
METAL 194 194 Magnesium.
METAL 219 219 Magnesium.
METAL 242 242 Magnesium.
BINDING 56 56 Substrate.
BINDING 162 162 Substrate.
BINDING 295 295 Substrate; via carbonyl oxygen.
STRAND 3 14 {ECO:0000244|PDB:4J1O}.
STRAND 20 22 {ECO:0000244|PDB:4J1O}.
STRAND 25 39 {ECO:0000244|PDB:4J1O}.
STRAND 44 49 {ECO:0000244|PDB:4J1O}.
STRAND 56 58 {ECO:0000244|PDB:4J1O}.
HELIX 61 71 {ECO:0000244|PDB:4J1O}.
HELIX 72 75 {ECO:0000244|PDB:4J1O}.
HELIX 83 91 {ECO:0000244|PDB:4J1O}.
HELIX 98 116 {ECO:0000244|PDB:4J1O}.
HELIX 120 123 {ECO:0000244|PDB:4J1O}.
STRAND 130 133 {ECO:0000244|PDB:4J1O}.
STRAND 136 138 {ECO:0000244|PDB:4J1O}.
HELIX 143 156 {ECO:0000244|PDB:4J1O}.
STRAND 159 164 {ECO:0000244|PDB:4J1O}.
HELIX 170 184 {ECO:0000244|PDB:4J1O}.
TURN 185 188 {ECO:0000244|PDB:4J1O}.
STRAND 190 194 {ECO:0000244|PDB:4J1O}.
HELIX 201 210 {ECO:0000244|PDB:4J1O}.
STRAND 216 220 {ECO:0000244|PDB:4J1O}.
STRAND 222 224 {ECO:0000244|PDB:4J1O}.
HELIX 225 231 {ECO:0000244|PDB:4J1O}.
HELIX 232 234 {ECO:0000244|PDB:4J1O}.
STRAND 239 242 {ECO:0000244|PDB:4J1O}.
HELIX 248 256 {ECO:0000244|PDB:4J1O}.
STRAND 261 266 {ECO:0000244|PDB:4J1O}.
HELIX 267 270 {ECO:0000244|PDB:4J1O}.
HELIX 273 285 {ECO:0000244|PDB:4J1O}.
STRAND 290 293 {ECO:0000244|PDB:4J1O}.
HELIX 299 309 {ECO:0000244|PDB:4J1O}.
HELIX 314 316 {ECO:0000244|PDB:4J1O}.
STRAND 317 319 {ECO:0000244|PDB:4J1O}.
HELIX 324 326 {ECO:0000244|PDB:4J1O}.
TURN 333 335 {ECO:0000244|PDB:4J1O}.
STRAND 343 345 {ECO:0000244|PDB:4J1O}.
STRAND 349 351 {ECO:0000244|PDB:4J1O}.
HELIX 358 360 {ECO:0000244|PDB:4J1O}.
STRAND 365 368 {ECO:0000244|PDB:4J1O}.
SEQUENCE 369 AA; 39382 MW; 31E3E18DBDF60A5A CRC64;
MKIAEIHVYA HDLPVKDGPY TIASSTVWSL QTTLVKIVAD SGLAGWGETC PVGPTYAPSH
ALGARAALAE MAPGLIGANP LQPLVLRRRM DGLLCGHNYA KAAIDIAAYD LMGKHYGVRV
ADLLGGVAAE RVPSYYATGI GQPDEIARIA AEKVAEGFPR LQIKIGGRPV EIDIETVRKV
WERIRGTGTR LAVDGNRSLP SRDALRLSRE CPEIPFVLEQ PCNTLEEIAA IRGRVQHGIY
LDESGEDLST VIRAAGQGLC DGFGMKLTRI GGLQQMAAFR DICEARALPH SCDDAWGGDI
IAAACTHIGA TVQPRLNEGV WVAQPYIAQP YDEENGIRIA GGHIDLPKGP GLGITPDESL
FGPPVASFS


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