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(-) Description

Title :  MECHANISM OF THE REACTION CATALYZED BY MANDELATE RACEMASE. 2. CRYSTAL STRUCTURE OF MANDELATE RACEMASE AT 2.5 ANGSTROMS RESOLUTION: IDENTIFICATION OF THE ACTIVE SITE AND POSSIBLE CATALYTIC RESIDUES
 
Authors :  D. J. Neidhart, G. A. Petsko
Date :  06 Jul 93  (Deposition) - 31 Jan 94  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Racemase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Neidhart, P. L. Howell, G. A. Petsko, V. M. Powers, R. S. Li, G. L. Kenyon, J. A. Gerlt
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.
Biochemistry V. 30 9264 1991
PubMed-ID: 1892834  |  Reference-DOI: 10.1021/BI00102A019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANDELATE RACEMASE
    Chains: A
    EC Number: 5.1.2.2
    Engineered: YES
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2SO48Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:195 , GLU A:221 , GLU A:247 , SO4 A:361 , HOH A:414 , HOH A:459BINDING SITE FOR RESIDUE MN A 360
2AC2SOFTWARESER A:139 , LYS A:164 , LYS A:166 , ASP A:195 , GLU A:221 , GLU A:247 , HIS A:297 , GLU A:317 , MN A:360 , HOH A:434 , HOH A:459 , HOH A:617BINDING SITE FOR RESIDUE SO4 A 361
3ACTAUTHORLYS A:166 , HIS A:297ACID/BASE CATALYSTS RESPONSIBLE FOR PROTON ABSTRACTION AND REDELIVERY IN THE RACEMIZATION REACTION
4CARAUTHORLYS A:164 , GLU A:317THE BINDING SITE FOR THE CARBOXYL GROUP OF SUBSTRATE. THESE RESIDUES FUNCTION, ALONG WITH THE METAL ION, AS ELECTROPHILIC CATALYSTS
5MTLAUTHORASP A:195 , GLU A:221 , GLU A:247DIRECT METAL ION LIGANDS

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MNR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2MNR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2MNR)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MR_MLE_1PS00908 Mandelate racemase / muconate lactonizing enzyme family signature 1.MANR_PSEPU103-128  1A:103-128
2MR_MLE_2PS00909 Mandelate racemase / muconate lactonizing enzyme family signature 2.MANR_PSEPU192-223  1A:192-223
Biological Unit 1 (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MR_MLE_1PS00908 Mandelate racemase / muconate lactonizing enzyme family signature 1.MANR_PSEPU103-128  8A:103-128
2MR_MLE_2PS00909 Mandelate racemase / muconate lactonizing enzyme family signature 2.MANR_PSEPU192-223  8A:192-223

(-) Exons   (0, 0)

(no "Exon" information available for 2MNR)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:357
 aligned with MANR_PSEPU | P11444 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:357
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       
           MANR_PSEPU     3 EVLITGLRTRAVNVPLAYPVHTAVGTVGTAPLVLIDLATSAGVVGHSYLFAYTPVALKSLKQLLDDMAAMIVNEPLAPVSLEAMLAKRFCLAGYTGLIRMAAAGIDMAAWDALGKVHETPLVKLLGANARPVQAYDSHSLDGVKLATERAVTAAELGFRAVKTKIGYPALDQDLAVVRSIRQAVGDDFGIMVDYNQSLDVPAAIKRSQALQQEGVTWIEEPTLQHDYEGHQRIQSKLNVPVQMGENWLGPEEMFKALSIGACRLAMPDAMKIGGVTGWIRASALAQQFGIPMSSHLFQEISAHLLAATPTAHWLERLDLAGSVIEPTLTFEGGNAVIPDLPGVGIIWREKEIGKYLV 359
               SCOP domains d2mnra2 A:3-132 Mandelate racemase                                                                                                d2mnra1 A:133-359 Mandelate racemase                                                                                                                                                                                                SCOP domains
               CATH domains 2mnrA01 A:3-120,A:351-358 Enolase-like, N-terminal domain                                                             2mnrA02 A:121-350 Enolase superfamily                                                                                                                                                                                                 2mnrA01 - CATH domains
               Pfam domains ---MR_MLE_N-2mnrA01 A:6-128                                                                                                   -------------------------------------------------MR_MLE-2mnrA02 A:178-246                                             ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eee..eee..eeeeeeeeee...eeeeeeee..hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhh......eeeeeee...hhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhh...eee.......hhhhhhhhh....eeee......hhhhhhhhhh...eeee..hhhh..hhhhhhhhhhhhhh..eeeee..hhhhhhhhh.....eeeee...hhhhh....eee..eee............hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------MR_MLE_1  PDB: A:103-128  ---------------------------------------------------------------MR_MLE_2  PDB: A:192-223        ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mnr A   3 EVLITGLRTRAVNVPLAYPVHTAVGTVGTAPLVLIDLATSAGVVGHSYLFAYTPVALKSLKQLLDDMAAMIVNEPLAPVSLEAMLAKRFCLAGYTGLIRMAAAGIDMAAWDALGKVHETPLVKLLGANARPVQAYDSHSLDGVKLATERAVTAAELGFRAVKTKIGYPALDQDLAVVRSIRQAVGDDFGIMVDYNQSLDVPAAIKRSQALQQEGVTWIEEPTLQHDYEGHQRIQSKLNVPVQMGENWLGPEEMFKALSIGACRLAMPDAMKIGGVTGWIRASALAQQFGIPMSSHLFQEISAHLLAATPTAHWLERLDLAGSVIEPTLTFEGGNAVIPDLPGVGIIWREKEIGKYLV 359
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Enolase_N (69)
(-)
Clan: Enolase_TIM (82)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (MANR_PSEPU | P11444)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0018838    mandelate racemase activity    Catalysis of the reaction: (S)-mandelate = (R)-mandelate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009063    cellular amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of amino acids, organic acids containing one or more amino substituents.
    GO:0019596    mandelate catabolic process    The chemical reactions and pathways resulting in the breakdown of mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic.
    GO:0018924    mandelate metabolic process    The chemical reactions and pathways involving mandelate, the anion of mandelic acid. Mandelic acid (alpha-hydroxybenzeneacetic acid) is an 8-carbon alpha-hydroxy acid (AHA) that is used in organic chemistry and as a urinary antiseptic.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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UniProtKB/Swiss-Prot
        MANR_PSEPU | P11444: 1dtn 1mdl 1mdr 1mns 1mra 3uxk 3uxl 4fp1 4hnc 4m6u 4x2p

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