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Protein

Mandelate racemase

Gene

mdlA

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalytic activityi

(S)-mandelate = (R)-mandelate.3 Publications

Cofactori

Mg2+3 PublicationsNote: Divalent metal ions. Magnesium seems to be the preferred ion.3 Publications

Pathway:i(R)-mandelate degradation

This protein is involved in step 1 of the subpathway that synthesizes benzoate from (R)-mandelate.Curated
Proteins known to be involved in the 4 steps of the subpathway in this organism are:
  1. Mandelate racemase (mdlA)
  2. (S)-mandelate dehydrogenase (mdlB)
  3. Benzoylformate decarboxylase (mdlC)
  4. NAD(P)-dependent benzaldehyde dehydrogenase (mdlD)
This subpathway is part of the pathway (R)-mandelate degradation, which is itself part of Aromatic compound metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes benzoate from (R)-mandelate, the pathway (R)-mandelate degradation and in Aromatic compound metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei166 – 1661Proton acceptor; specific for S-mandelate
Metal bindingi195 – 1951Magnesium1 Publication2 Publications
Metal bindingi221 – 2211Magnesium1 Publication2 Publications
Metal bindingi247 – 2471Magnesium1 Publication2 Publications
Active sitei297 – 2971Proton acceptor; specific for R-mandelate
Binding sitei317 – 3171Substrate1 Publication2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Mandelate pathway

Keywords - Ligandi

Magnesium, Metal-binding

Enzyme and pathway databases

BioCyciMetaCyc:MONOMER-2421.
BRENDAi5.1.2.2. 5092.
UniPathwayiUPA00873; UER00852.

Names & Taxonomyi

Protein namesi
Recommended name:
Mandelate racemase (EC:5.1.2.23 Publications)
Short name:
MR
Gene namesi
Name:mdlA
OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)
Taxonomic identifieri303 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi166 – 1661K → A, M or Q: Loss of activity. 1 Publication
Mutagenesisi297 – 2971H → N: Loss of activity. 1 Publication
Mutagenesisi317 – 3171E → Q: Reduces activity 10000-fold. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 359359Mandelate racemasePRO_0000171247Add
BLAST

Interactioni

Subunit structurei

Homooctamer.1 Publication

Structurei

Secondary structure

1
359
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi5 – 1612Combined sources
Beta strandi22 – 243Combined sources
Beta strandi27 – 293Combined sources
Beta strandi31 – 4111Combined sources
Beta strandi46 – 527Combined sources
Helixi56 – 583Combined sources
Helixi59 – 7315Combined sources
Beta strandi76 – 783Combined sources
Helixi80 – 9011Combined sources
Turni91 – 944Combined sources
Helixi98 – 11821Combined sources
Helixi123 – 1264Combined sources
Beta strandi134 – 1396Combined sources
Helixi144 – 15714Combined sources
Beta strandi161 – 1666Combined sources
Helixi172 – 18615Combined sources
Beta strandi188 – 1958Combined sources
Helixi202 – 21413Combined sources
Beta strandi218 – 2214Combined sources
Helixi229 – 2368Combined sources
Beta strandi243 – 2453Combined sources
Helixi252 – 2609Combined sources
Beta strandi265 – 2673Combined sources
Turni271 – 2755Combined sources
Helixi276 – 29015Combined sources
Helixi300 – 3089Combined sources
Beta strandi316 – 3183Combined sources
Turni321 – 3255Combined sources
Beta strandi330 – 3334Combined sources
Beta strandi336 – 3383Combined sources
Beta strandi341 – 3444Combined sources
Helixi351 – 3577Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DTNX-ray2.10A1-359[»]
1MDLX-ray1.85A1-359[»]
1MDRX-ray2.10A1-359[»]
1MNSX-ray2.00A3-359[»]
1MRAX-ray2.10A1-359[»]
2MNRX-ray1.90A3-359[»]
3UXKX-ray2.20A/B/C/D1-359[»]
3UXLX-ray2.20A/B/C/D1-359[»]
4FP1X-ray1.68A/B1-359[»]
4HNCX-ray1.89A/B1-359[»]
4M6UX-ray1.80A/B1-359[»]
ProteinModelPortaliP11444.
SMRiP11444. Positions 3-359.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11444.

Family & Domainsi

Sequence similaritiesi

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N-like.
IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N_dom.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
PfamiPF01188. MR_MLE. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]
SMARTiSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMiSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.
PROSITEiPS00908. MR_MLE_1. 1 hit.
PS00909. MR_MLE_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P11444-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSEVLITGLR TRAVNVPLAY PVHTAVGTVG TAPLVLIDLA TSAGVVGHSY
60 70 80 90 100
LFAYTPVALK SLKQLLDDMA AMIVNEPLAP VSLEAMLAKR FCLAGYTGLI
110 120 130 140 150
RMAAAGIDMA AWDALGKVHE TPLVKLLGAN ARPVQAYDSH SLDGVKLATE
160 170 180 190 200
RAVTAAELGF RAVKTKIGYP ALDQDLAVVR SIRQAVGDDF GIMVDYNQSL
210 220 230 240 250
DVPAAIKRSQ ALQQEGVTWI EEPTLQHDYE GHQRIQSKLN VPVQMGENWL
260 270 280 290 300
GPEEMFKALS IGACRLAMPD AMKIGGVTGW IRASALAQQF GIPMSSHLFQ
310 320 330 340 350
EISAHLLAAT PTAHWLERLD LAGSVIEPTL TFEGGNAVIP DLPGVGIIWR

EKEIGKYLV
Length:359
Mass (Da):38,565
Last modified:October 1, 1989 - v1
Checksum:i1C105BCA021F4028
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19043 Genomic DNA. Translation: AAA25887.1.
AY143338 Genomic DNA. Translation: AAC15504.1.
PIRiA28700.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M19043 Genomic DNA. Translation: AAA25887.1.
AY143338 Genomic DNA. Translation: AAC15504.1.
PIRiA28700.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1DTNX-ray2.10A1-359[»]
1MDLX-ray1.85A1-359[»]
1MDRX-ray2.10A1-359[»]
1MNSX-ray2.00A3-359[»]
1MRAX-ray2.10A1-359[»]
2MNRX-ray1.90A3-359[»]
3UXKX-ray2.20A/B/C/D1-359[»]
3UXLX-ray2.20A/B/C/D1-359[»]
4FP1X-ray1.68A/B1-359[»]
4HNCX-ray1.89A/B1-359[»]
4M6UX-ray1.80A/B1-359[»]
ProteinModelPortaliP11444.
SMRiP11444. Positions 3-359.
ModBaseiSearch...
MobiDBiSearch...

Chemistry

BindingDBiP11444.
ChEMBLiCHEMBL4739.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00873; UER00852.
BioCyciMetaCyc:MONOMER-2421.
BRENDAi5.1.2.2. 5092.

Miscellaneous databases

EvolutionaryTraceiP11444.

Family and domain databases

Gene3Di3.20.20.120. 1 hit.
3.30.390.10. 1 hit.
InterProiIPR029065. Enolase_C-like.
IPR029017. Enolase_N-like.
IPR018110. Mandel_Rmase/mucon_lact_enz_CS.
IPR013342. Mandelate_racemase_C.
IPR013341. Mandelate_racemase_N_dom.
IPR001354. MR/MLE/MAL.
[Graphical view]
PANTHERiPTHR13794. PTHR13794. 1 hit.
PfamiPF01188. MR_MLE. 1 hit.
PF02746. MR_MLE_N. 1 hit.
[Graphical view]
SMARTiSM00922. MR_MLE. 1 hit.
[Graphical view]
SUPFAMiSSF51604. SSF51604. 1 hit.
SSF54826. SSF54826. 1 hit.
PROSITEiPS00908. MR_MLE_1. 1 hit.
PS00909. MR_MLE_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  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, CATALYTIC ACTIVITY.
  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 (1.90 ANGSTROMS) OF 3-359 IN COMPLEX WITH MANGANESE, COFACTOR.
  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 IN COMPLEX WITH MAGNESIUM, COFACTOR, MUTAGENESIS OF GLU-317, CATALYTIC ACTIVITY.
  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 AND MAGNESIUM, COFACTOR, MUTAGENESIS OF LYS-166, CATALYTIC ACTIVITY.

Entry informationi

Entry nameiMANR_PSEPU
AccessioniPrimary (citable) accession number: P11444
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: October 1, 1989
Last modified: July 22, 2015
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.