P11444 (MANR_PSEPU) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Mandelate racemase
Short name=MR
EC=5.1.2.2

Gene names

Name:

mdlA

Organism

Pseudomonas putida (Arthrobacter siderocapsulatus)

Taxonomic identifier

303 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Gammaproteobacteria › Pseudomonadales › Pseudomonadaceae › Pseudomonas › Pseudomonas putida group

Protein attributes

Sequence length	359 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	(S)-mandelate = (R)-mandelate.
Cofactor	Divalent metal ions. Magnesium seems to be the preferred ion.
Pathway	Aromatic compound metabolism; (R)-mandelate degradation; benzoate from (R)-mandelate: step 1/4.
Subunit structure	Homooctamer.
Sequence similarities	Belongs to the mandelate racemase/muconate lactonizing enzyme family.

Ontologies

Keywords
Biological process	Mandelate pathway
Ligand	Magnesium Metal-binding
Molecular function	Isomerase
Technical term	3D-structure
Gene Ontology (GO)
Biological_process	cellular amino acid catabolic process Inferred from electronic annotation. Source: InterPro mandelate catabolic process Inferred from electronic annotation. Source: UniProtKB-UniPathway
Molecular_function	mandelate racemase activity Inferred from electronic annotation. Source: EC metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 359

359

Mandelate racemase

PRO_0000171247

Sites

Active site

166

1

Proton acceptor; specific for S-mandelate

Active site

297

1

Proton acceptor; specific for R-mandelate

Metal binding

195

1

Magnesium

Metal binding

221

1

Magnesium

Metal binding

247

1

Magnesium

Binding site

317

1

Substrate

Experimental info

Mutagenesis

166

1

K → A, M or Q: Loss of activity. Ref.7

Mutagenesis

297

1

H → N: Loss of activity. Ref.4

Mutagenesis

317

1

E → Q: Reduces activity 10000-fold.

Secondary structure

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359

Helix Strand Turn

Details...

Beta strand

5 – 23

19

Beta strand

28 – 41

14

Beta strand

46 – 52

7

Helix

56 – 58

3

Helix

59 – 73

15

Beta strand

76 – 78

3

Helix

80 – 90

11

Turn

91 – 94

4

Helix

98 – 118

21

Helix

123 – 126

4

Beta strand

134 – 139

6

Helix

144 – 157

14

Beta strand

161 – 166

6

Helix

172 – 186

15

Beta strand

188 – 195

8

Helix

202 – 215

14

Beta strand

218 – 221

4

Helix

229 – 237

9

Beta strand

243 – 245

3

Helix

252 – 260

9

Beta strand

265 – 267

3

Turn

271 – 275

5

Helix

276 – 289

14

Helix

300 – 308

9

Beta strand

316 – 318

3

Turn

323 – 325

3

Beta strand

330 – 333

4

Beta strand

336 – 338

3

Beta strand

341 – 344

4

Helix

351 – 357

7

Sequences

	Sequence		Length	Mass (Da)
	P11444 [UniParc]. Last modified October 1, 1989. Version 1. Checksum: 1C105BCA021F4028	FASTA	359	38,565
	10 20 30 40 50 60 MSEVLITGLR TRAVNVPLAY PVHTAVGTVG TAPLVLIDLA TSAGVVGHSY LFAYTPVALK 70 80 90 100 110 120 SLKQLLDDMA AMIVNEPLAP VSLEAMLAKR FCLAGYTGLI RMAAAGIDMA AWDALGKVHE 130 140 150 160 170 180 TPLVKLLGAN ARPVQAYDSH SLDGVKLATE RAVTAAELGF RAVKTKIGYP ALDQDLAVVR 190 200 210 220 230 240 SIRQAVGDDF GIMVDYNQSL DVPAAIKRSQ ALQQEGVTWI EEPTLQHDYE GHQRIQSKLN 250 260 270 280 290 300 VPVQMGENWL GPEEMFKALS IGACRLAMPD AMKIGGVTGW IRASALAQQF GIPMSSHLFQ 310 320 330 340 350 EISAHLLAAT PTAHWLERLD LAGSVIEPTL TFEGGNAVIP DLPGVGIIWR EKEIGKYLV

References

[1]	"Cloning, DNA sequence analysis, and expression in Escherichia coli of the gene for mandelate racemase from Pseudomonas putida." Ransom S.C., Gerlt J.A., Powers V.M., Kenyon G.L. Biochemistry 27:540-545(1988) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 12633 / DSM 291 / JCM 13063 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90.
[2]	"Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli." Tsou A.Y., Ransom S.C., Gerlt J.A., Buechter D.D., Babbitt P.C., Kenyon G.L. Biochemistry 29:9856-9862(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 12633 / DSM 291 / JCM 13063 / NCIMB 9494 / NCTC 10936 / VKM B-2187 / Stanier 90.
[3]	"Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous." Neidhart D.J., Kenyon G.L., Gerlt J.A., Petsko G.A. Nature 347:692-694(1990) [PubMed] [Europe PMC] [Abstract] Cited for: SIMILARITY TO MLE.
[4]	"Mechanism of the reaction catalyzed by mandelate racemase. 3. Asymmetry in reactions catalyzed by the H297N mutant." Landro J.A., Kallarakal A.T., Ransom S.C., Gerlt J.A., Kozarich J.W., Neidhart D.J., Kenyon G.L. Biochemistry 30:9274-9281(1991) [PubMed] [Europe PMC] [Abstract] Cited for: MUTAGENESIS OF HIS-297.
[5]	"Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues." Neidhart D.J., Howell P.L., Petsko G.A., Powers V.M., Li R.S., Kenyon G.L., Gerlt J.A. Biochemistry 30:9264-9273(1991) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
[6]	"Mechanism of the reaction catalyzed by mandelate racemase: importance of electrophilic catalysis by glutamic acid 317." Mitra B., Kallarakal A.T., Kozarich J.W., Gerlt J.A., Clifton J.G., Petsko G.A., Kenyon G.L. Biochemistry 34:2777-2787(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF MUTANT GLN-317.
[7]	"Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the K166R mutant." Kallarakal A.T., Mitra B., Kozarich J.W., Gerlt J.A., Clifton J.G., Petsko G.A., Kenyon G.L. Biochemistry 34:2788-2797(1995) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF MUTANT ARG-166 IN COMPLEX WITH SUBSTRATE, MUTAGENESIS OF LYS-166.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M19043 Genomic DNA. Translation: AAA25887.1.
AY143338 Genomic DNA. Translation: AAC15504.1.

PIR

A28700.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1DTN	X-ray	2.10	A	1-359	[»]
1MDL	X-ray	1.85	A	1-359	[»]
1MDR	X-ray	2.10	A	1-359	[»]
1MNS	X-ray	2.00	A	3-359	[»]
1MRA	X-ray	2.10	A	1-359	[»]
2MNR	X-ray	1.90	A	3-359	[»]
3UXK	X-ray	2.20	A/B/C/D	1-359	[»]
3UXL	X-ray	2.20	A/B/C/D	1-359	[»]

ProteinModelPortal

P11444.

SMR

P11444. Positions 3-359.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

BioCyc

MetaCyc:MONOMER-2421.

UniPathway

UPA00873; UER00852.

Family and domain databases

InterPro

IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N.
IPR001354. MR_MLE.
[Graphical view]

PANTHER

PTHR13794. PTHR13794. 1 hit.

Pfam

PF01188. MR_MLE. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]

SMART

SM00922. MR_MLE. 1 hit.
[Graphical view]

PROSITE

PS00908. MR_MLE_1. 1 hit.
PS00909. MR_MLE_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

P11444.

ChEMBL

CHEMBL4739.

EvolutionaryTrace

P11444.

Entry information

Entry name

MANR_PSEPU

Accession

Primary (citable) accession number: P11444

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1989
Last sequence update:	October 1, 1989
Last modified:	April 3, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program