MANR_PSEPU
ID MANR_PSEPU Reviewed; 359 AA.
AC P11444;
DT 01-OCT-1989, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1989, sequence version 1.
DT 03-AUG-2022, entry version 128.
DE RecName: Full=Mandelate racemase;
DE Short=MR;
DE EC=5.1.2.2 {ECO:0000269|PubMed:1909893, ECO:0000269|PubMed:7893689, ECO:0000269|PubMed:7893690};
GN Name=mdlA;
OS Pseudomonas putida (Arthrobacter siderocapsulatus).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=303;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 12633 / DSM 291 / JCM 13063 / CCUG 12690 / LMG 2257 / NBRC
RC 14164 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90;
RX PubMed=2831968; DOI=10.1021/bi00402a006;
RA Ransom S.C., Gerlt J.A., Powers V.M., Kenyon G.L.;
RT "Cloning, DNA sequence analysis, and expression in Escherichia coli of the
RT gene for mandelate racemase from Pseudomonas putida.";
RL Biochemistry 27:540-545(1988).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 12633 / DSM 291 / JCM 13063 / CCUG 12690 / LMG 2257 / NBRC
RC 14164 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90;
RX PubMed=2271624; DOI=10.1021/bi00494a015;
RA Tsou A.Y., Ransom S.C., Gerlt J.A., Buechter D.D., Babbitt P.C.,
RA Kenyon G.L.;
RT "Mandelate pathway of Pseudomonas putida: sequence relationships involving
RT mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate
RT decarboxylase and expression of benzoylformate decarboxylase in Escherichia
RT coli.";
RL Biochemistry 29:9856-9862(1990).
RN [3]
RP SIMILARITY TO MLE.
RX PubMed=2215699; DOI=10.1038/347692a0;
RA Neidhart D.J., Kenyon G.L., Gerlt J.A., Petsko G.A.;
RT "Mandelate racemase and muconate lactonizing enzyme are mechanistically
RT distinct and structurally homologous.";
RL Nature 347:692-694(1990).
RN [4]
RP MUTAGENESIS OF HIS-297, AND CATALYTIC ACTIVITY.
RX PubMed=1909893; DOI=10.1021/bi00102a020;
RA Landro J.A., Kallarakal A.T., Ransom S.C., Gerlt J.A., Kozarich J.W.,
RA Neidhart D.J., Kenyon G.L.;
RT "Mechanism of the reaction catalyzed by mandelate racemase. 3. Asymmetry in
RT reactions catalyzed by the H297N mutant.";
RL Biochemistry 30:9274-9281(1991).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 3-359 IN COMPLEX WITH MANGANESE,
RP AND COFACTOR.
RX PubMed=1892834; DOI=10.1021/bi00102a019;
RA Neidhart D.J., Howell P.L., Petsko G.A., Powers V.M., Li R.S., Kenyon G.L.,
RA Gerlt J.A.;
RT "Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal
RT structure of mandelate racemase at 2.5-A resolution: identification of the
RT active site and possible catalytic residues.";
RL Biochemistry 30:9264-9273(1991).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF MUTANT GLN-317 IN COMPLEX WITH
RP MAGNESIUM, COFACTOR, MUTAGENESIS OF GLU-317, AND CATALYTIC ACTIVITY.
RX PubMed=7893689; DOI=10.1021/bi00009a006;
RA Mitra B., Kallarakal A.T., Kozarich J.W., Gerlt J.A., Clifton J.G.,
RA Petsko G.A., Kenyon G.L.;
RT "Mechanism of the reaction catalyzed by mandelate racemase: importance of
RT electrophilic catalysis by glutamic acid 317.";
RL Biochemistry 34:2777-2787(1995).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF MUTANT ARG-166 IN COMPLEX WITH
RP SUBSTRATE AND MAGNESIUM, COFACTOR, MUTAGENESIS OF LYS-166, AND CATALYTIC
RP ACTIVITY.
RX PubMed=7893690; DOI=10.1021/bi00009a007;
RA Kallarakal A.T., Mitra B., Kozarich J.W., Gerlt J.A., Clifton J.G.,
RA Petsko G.A., Kenyon G.L.;
RT "Mechanism of the reaction catalyzed by mandelate racemase: structure and
RT mechanistic properties of the K166R mutant.";
RL Biochemistry 34:2788-2797(1995).
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(S)-mandelate = (R)-mandelate; Xref=Rhea:RHEA:13945,
CC ChEBI:CHEBI:17756, ChEBI:CHEBI:32382; EC=5.1.2.2;
CC Evidence={ECO:0000269|PubMed:1909893, ECO:0000269|PubMed:7893689,
CC ECO:0000269|PubMed:7893690};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:1892834, ECO:0000269|PubMed:7893689,
CC ECO:0000269|PubMed:7893690};
CC Note=Divalent metal ions. Magnesium seems to be the preferred ion.
CC {ECO:0000269|PubMed:1892834, ECO:0000269|PubMed:7893689,
CC ECO:0000269|PubMed:7893690};
CC -!- PATHWAY: Aromatic compound metabolism; (R)-mandelate degradation;
CC benzoate from (R)-mandelate: step 1/4. {ECO:0000305}.
CC -!- SUBUNIT: Homooctamer. {ECO:0000269|PubMed:7893690}.
CC -!- SIMILARITY: Belongs to the mandelate racemase/muconate lactonizing
CC enzyme family. {ECO:0000305}.
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DR EMBL; M19043; AAA25887.1; -; Genomic_DNA.
DR EMBL; AY143338; AAC15504.1; -; Genomic_DNA.
DR PIR; A28700; A28700.
DR RefSeq; WP_016501748.1; NZ_UGUX01000003.1.
DR PDB; 1DTN; X-ray; 2.10 A; A=1-359.
DR PDB; 1MDL; X-ray; 1.85 A; A=1-359.
DR PDB; 1MDR; X-ray; 2.10 A; A=1-359.
DR PDB; 1MNS; X-ray; 2.00 A; A=3-359.
DR PDB; 1MRA; X-ray; 2.10 A; A=1-359.
DR PDB; 2MNR; X-ray; 1.90 A; A=3-359.
DR PDB; 3UXK; X-ray; 2.20 A; A/B/C/D=1-359.
DR PDB; 3UXL; X-ray; 2.20 A; A/B/C/D=1-359.
DR PDB; 4FP1; X-ray; 1.68 A; A/B=1-359.
DR PDB; 4HNC; X-ray; 1.89 A; A/B=1-359.
DR PDB; 4M6U; X-ray; 1.80 A; A/B=1-359.
DR PDB; 4X2P; X-ray; 1.65 A; A=1-359.
DR PDB; 6VIM; X-ray; 2.00 A; A/B/C/D/E/F/G/H=1-359.
DR PDB; 7MQX; X-ray; 1.91 A; A/B/C/D/E/F/G/H=1-359.
DR PDBsum; 1DTN; -.
DR PDBsum; 1MDL; -.
DR PDBsum; 1MDR; -.
DR PDBsum; 1MNS; -.
DR PDBsum; 1MRA; -.
DR PDBsum; 2MNR; -.
DR PDBsum; 3UXK; -.
DR PDBsum; 3UXL; -.
DR PDBsum; 4FP1; -.
DR PDBsum; 4HNC; -.
DR PDBsum; 4M6U; -.
DR PDBsum; 4X2P; -.
DR PDBsum; 6VIM; -.
DR PDBsum; 7MQX; -.
DR AlphaFoldDB; P11444; -.
DR SMR; P11444; -.
DR BindingDB; P11444; -.
DR ChEMBL; CHEMBL4739; -.
DR DrugBank; DB02280; (R)-Mandelic acid.
DR DrugBank; DB07381; (S)-atrolactic acid.
DR DrugBank; DB03357; (S)-Mandelic acid.
DR PRIDE; P11444; -.
DR GeneID; 45526288; -.
DR BioCyc; MetaCyc:MON-2421; -.
DR BRENDA; 5.1.2.2; 5092.
DR UniPathway; UPA00873; UER00852.
DR EvolutionaryTrace; P11444; -.
DR GO; GO:0018838; F:mandelate racemase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0009063; P:cellular amino acid catabolic process; IEA:InterPro.
DR GO; GO:0019596; P:mandelate catabolic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.20.20.120; -; 1.
DR Gene3D; 3.30.390.10; -; 1.
DR InterPro; IPR036849; Enolase-like_C_sf.
DR InterPro; IPR029017; Enolase-like_N.
DR InterPro; IPR029065; Enolase_C-like.
DR InterPro; IPR018110; Mandel_Rmase/mucon_lact_enz_CS.
DR InterPro; IPR015654; Mandelate_racemase.
DR InterPro; IPR013342; Mandelate_racemase_C.
DR InterPro; IPR013341; Mandelate_racemase_N_dom.
DR Pfam; PF13378; MR_MLE_C; 1.
DR Pfam; PF02746; MR_MLE_N; 1.
DR SFLD; SFLDF00004; mandelate_racemase; 1.
DR SMART; SM00922; MR_MLE; 1.
DR SUPFAM; SSF51604; SSF51604; 1.
DR SUPFAM; SSF54826; SSF54826; 1.
DR PROSITE; PS00908; MR_MLE_1; 1.
DR PROSITE; PS00909; MR_MLE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Isomerase; Magnesium; Mandelate pathway; Metal-binding.
FT CHAIN 1..359
FT /note="Mandelate racemase"
FT /id="PRO_0000171247"
FT ACT_SITE 166
FT /note="Proton acceptor; specific for S-mandelate"
FT ACT_SITE 297
FT /note="Proton acceptor; specific for R-mandelate"
FT BINDING 195
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:7893689,
FT ECO:0000269|PubMed:7893690, ECO:0000305|PubMed:1892834"
FT BINDING 221
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:7893689,
FT ECO:0000269|PubMed:7893690, ECO:0000305|PubMed:1892834"
FT BINDING 247
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:7893689,
FT ECO:0000269|PubMed:7893690, ECO:0000305|PubMed:1892834"
FT BINDING 317
FT /ligand="substrate"
FT /evidence="ECO:0000269|PubMed:7893689,
FT ECO:0000269|PubMed:7893690, ECO:0000305|PubMed:1892834"
FT MUTAGEN 166
FT /note="K->A,M,Q: Loss of activity."
FT /evidence="ECO:0000269|PubMed:7893690"
FT MUTAGEN 297
FT /note="H->N: Loss of activity."
FT /evidence="ECO:0000269|PubMed:1909893"
FT MUTAGEN 317
FT /note="E->Q: Reduces activity 10000-fold."
FT /evidence="ECO:0000269|PubMed:7893689"
FT STRAND 5..23
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 28..41
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 46..52
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 56..58
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 59..73
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 80..90
FT /evidence="ECO:0007829|PDB:4X2P"
FT TURN 91..94
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 98..118
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 123..126
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 134..139
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 144..157
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 172..186
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 188..195
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 202..215
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 218..221
FT /evidence="ECO:0007829|PDB:4M6U"
FT HELIX 229..237
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 243..245
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 252..260
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 265..267
FT /evidence="ECO:0007829|PDB:4X2P"
FT TURN 271..275
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 276..290
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 300..308
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 316..318
FT /evidence="ECO:0007829|PDB:4X2P"
FT TURN 321..325
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 330..333
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 336..338
FT /evidence="ECO:0007829|PDB:4X2P"
FT STRAND 341..344
FT /evidence="ECO:0007829|PDB:4X2P"
FT HELIX 351..357
FT /evidence="ECO:0007829|PDB:4X2P"
SQ SEQUENCE 359 AA; 38565 MW; 1C105BCA021F4028 CRC64;
MSEVLITGLR TRAVNVPLAY PVHTAVGTVG TAPLVLIDLA TSAGVVGHSY LFAYTPVALK
SLKQLLDDMA AMIVNEPLAP VSLEAMLAKR FCLAGYTGLI RMAAAGIDMA AWDALGKVHE
TPLVKLLGAN ARPVQAYDSH SLDGVKLATE RAVTAAELGF RAVKTKIGYP ALDQDLAVVR
SIRQAVGDDF GIMVDYNQSL DVPAAIKRSQ ALQQEGVTWI EEPTLQHDYE GHQRIQSKLN
VPVQMGENWL GPEEMFKALS IGACRLAMPD AMKIGGVTGW IRASALAQQF GIPMSSHLFQ
EISAHLLAAT PTAHWLERLD LAGSVIEPTL TFEGGNAVIP DLPGVGIIWR EKEIGKYLV
