HPBD_SALBH
ID HPBD_SALBH Reviewed; 367 AA.
AC Q0FPQ4;
DT 19-FEB-2014, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 03-AUG-2022, entry version 72.
DE RecName: Full=4-hydroxyproline betaine 2-epimerase;
DE Short=Hyp-B 2-epimerase;
DE EC=5.1.1.22 {ECO:0000269|PubMed:24056934};
DE AltName: Full=(4R)-4-hydroxyproline betaine 2-epimerase;
GN Name=hpbD; ORFNames=R2601_01638;
OS Salipiger bermudensis (strain DSM 26914 / JCM 13377 / KCTC 12554 /
OS HTCC2601) (Pelagibaca bermudensis).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Roseobacteraceae; Salipiger.
OX NCBI_TaxID=314265;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 26914 / JCM 13377 / KCTC 12554 / HTCC2601;
RX PubMed=20729358; DOI=10.1128/jb.00873-10;
RA Thrash J.C., Cho J.C., Ferriera S., Johnson J., Vergin K.L.,
RA Giovannoni S.J.;
RT "Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter
RT alkaliphilus HTCC2654T, the type strains of two marine Roseobacter
RT genera.";
RL J. Bacteriol. 192:5552-5553(2010).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) IN COMPLEXES WITH MAGNESIUM AND
RP HYDROXYPROLINE BETAINE, FUNCTION, CATALYTIC ACTIVITY, KINETIC PARAMETERS,
RP COFACTOR, GENE NAME, AND PATHWAY.
RC STRAIN=DSM 26914 / JCM 13377 / KCTC 12554 / HTCC2601;
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).
CC -!- FUNCTION: Catalyzes the 2-epimerization of trans-4-hydroxy-L-proline
CC betaine (tHyp-B) to cis-4-hydroxy-D-proline betaine (cHyp-B). Is
CC involved in a catabolic pathway that degrades tHyp-B to alpha-
CC ketoglutarate. This pathway would permit the utilization of tHyp-B as a
CC carbon and nitrogen source in the absence of osmotic stress, since
CC tHyp-B functions as an osmolyte and is not catabolized when it is
CC needed as osmoprotectant. To a lesser extent, can also catalyze the
CC racemization of L-proline betaine. {ECO:0000269|PubMed:24056934}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=trans-4-hydroxy-L-proline betaine = cis-4-hydroxy-D-proline
CC betaine; Xref=Rhea:RHEA:47544, ChEBI:CHEBI:85533, ChEBI:CHEBI:85534;
CC EC=5.1.1.22; Evidence={ECO:0000269|PubMed:24056934};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=L-proline betaine = D-proline betaine; Xref=Rhea:RHEA:51884,
CC ChEBI:CHEBI:35280, ChEBI:CHEBI:134398; EC=5.1.1.22;
CC Evidence={ECO:0000269|PubMed:24056934};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:24056934};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:24056934};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=42 mM for trans-4-hydroxy-L-proline betaine
CC {ECO:0000269|PubMed:24056934};
CC KM=8 mM for L-proline betaine {ECO:0000269|PubMed:24056934};
CC Note=kcat is 330 sec(-1) with trans-4-hydroxy-L-proline betaine as
CC substrate and 5.3 sec(-1) with L-proline betaine as substrate.;
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; AATQ01000017; EAU46159.1; -; Genomic_DNA.
DR RefSeq; WP_007801489.1; NZ_DS022277.1.
DR PDB; 2PMQ; X-ray; 1.72 A; A/B=2-367.
DR PDB; 4H2H; X-ray; 1.70 A; A/B/C/D/E/F/G/H=2-367.
DR PDBsum; 2PMQ; -.
DR PDBsum; 4H2H; -.
DR AlphaFoldDB; Q0FPQ4; -.
DR SMR; Q0FPQ4; -.
DR DIP; DIP-60607N; -.
DR STRING; 314265.R2601_01638; -.
DR EnsemblBacteria; EAU46159; EAU46159; R2601_01638.
DR eggNOG; COG4948; Bacteria.
DR HOGENOM; CLU_030273_4_5_5; -.
DR OrthoDB; 951991at2; -.
DR BioCyc; MetaCyc:MON-18940; -.
DR BRENDA; 5.1.1.22; 15071.
DR EvolutionaryTrace; Q0FPQ4; -.
DR Proteomes; UP000006230; Unassembled WGS sequence.
DR GO; GO:0000287; F:magnesium ion binding; IDA:UniProtKB.
DR GO; GO:0036361; F:racemase activity, acting on amino acids and derivatives; IDA:UniProtKB.
DR GO; GO:0016855; F:racemase and epimerase activity, acting on amino acids and derivatives; IDA:CACAO.
DR GO; GO:0006579; P:amino-acid betaine catabolic process; ISS:UniProtKB.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR InterPro; IPR034622; 4R-hPro_betaine_2-epimerase.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR034593; Mandelate_racemase_DgoD-like.
DR InterPro; IPR013341; Mandelate_racemase_N_dom.
DR PANTHER; PTHR48080; PTHR48080; 1.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDF00556; 4R-hydroxyproline_betaine_2-ep; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Magnesium; Metal-binding; Reference proteome.
FT CHAIN 1..367
FT /note="4-hydroxyproline betaine 2-epimerase"
FT /id="PRO_0000425278"
FT ACT_SITE 163
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT ACT_SITE 265
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250"
FT BINDING 56
FT /ligand="substrate"
FT BINDING 161
FT /ligand="substrate"
FT BINDING 193
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 218
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 241
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT BINDING 294
FT /ligand="substrate"
FT STRAND 2..15
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 27..39
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 52..58
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 61..73
FT /evidence="ECO:0007829|PDB:4H2H"
FT TURN 74..77
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 79..81
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 82..92
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 97..115
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 119..122
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 134..137
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 142..155
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 158..163
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 169..183
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 189..193
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 200..209
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 215..219
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 221..223
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 224..230
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 231..233
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 247..255
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 260..262
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 266..269
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 272..285
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 298..308
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 313..315
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:4H2H"
FT HELIX 323..325
FT /evidence="ECO:0007829|PDB:4H2H"
FT TURN 332..334
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 342..344
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 348..350
FT /evidence="ECO:0007829|PDB:4H2H"
FT TURN 357..360
FT /evidence="ECO:0007829|PDB:4H2H"
FT STRAND 364..367
FT /evidence="ECO:0007829|PDB:4H2H"
SQ SEQUENCE 367 AA; 39558 MW; 6377860F2A17B87E CRC64;
MKIAEIQLFQ HDLPVVNGPY RIASGDVWSL TTTIVKIIAE DGTIGWGETC PVGPTYAEAH
AGGALAALEV LASGLAGAEA LPLPLHTRMD SLLCGHNYAK SALDIAVHDL WGKRLGVPVH
ELLGGALTDS VSSYYSLGVM EPDEAARQAL EKQREGYSRL QVKLGARPIE IDIEAIRKVW
EAVRGTGIAL AADGNRGWTT RDALRFSREC PDIPFVMEQP CNSFEDLEAI RPLCHHALYM
DEDGTSLNTV ITAAATSLVD GFGMKVSRIG GLQHMRAFRD FCAARNLPHT CDDAWGGDIV
SAACTHIAST VLPRLMEGAW LAQPYVAEHY DAENGVRIEG GRIRVPQGPG LGLTIDPERF
GPPLFSA
