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(-) Description

Title :  THE CRYSTAL STRUCTURE OF D-MANDELATE DEHYDROGENASE
 
Authors :  A. Miyanaga, S. Fujisawa, N. Furukawa, K. Arai, M. Nakajima, H. Taguchi
Date :  19 Jul 13  (Deposition) - 23 Jul 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rosmann Fold, Dehydrogenase, Nadh Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Miyanaga, S. Fujisawa, N. Furukawa, K. Arai, M. Nakajima, H. Taguch
The Crystal Structure Of D-Mandelate Dehydrogenase Reveals Its Distinct Substrate And Coenzyme Recognition Mechanisms From Those Of 2-Ketopantoate Reductase.
Biochem. Biophys. Res. Commun. V. 439 109 2013
PubMed-ID: 23954635  |  Reference-DOI: 10.1016/J.BBRC.2013.08.019

(-) Compounds

Molecule 1 - 2-DEHYDROPANTOATE 2-REDUCTASE
    Chains: A, B
    EC Number: 1.1.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PLG1-0150
    Organism Scientific: ENTEROCOCCUS FAECIUM
    Organism Taxid: 1352
    Strain: IAM10071

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3WFI)

(-) Sites  (0, 0)

(no "Site" information available for 3WFI)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WFI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:49 -Gly A:50
2Asn B:49 -Gly B:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WFI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WFI)

(-) Exons   (0, 0)

(no "Exon" information available for 3WFI)

(-) Sequences/Alignments

Asymmetric/Biological 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:311
 aligned with E3USM3_ENTFC | E3USM3 from UniProtKB/TrEMBL  Length:312

    Alignment length:311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 
         E3USM3_ENTFC     1 MKIAIAGAGAMGSRFGLMLHQSGNEVLLIDGWAEHVQQIKEHGLQANFNGKEVEAKLPIVLQSEVEKEDQVDLIILFTKAMQLEKMLQDIQSLIKKDTEVLCLLNGIGHEDIIEKFVPMENIYIGNTMWTAGLEGPGQVKLFGSGSVELQNLGDGKEAAAKKLADKLSESGLNAHFSDNIHYSIYRKACVNGTMNGLCTILDVNMAELGKTSTAHKMVATIVNEFAKVAAVEKIELDVPEVIAHCESCFDPETIGLHYPSMYQDLIKNHRLTEIDYINGAISRKGKKYGVATPYCDFLTELVHAKEDSLNV 311
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhheeeee..eeeee...eee.hhh.....eeeeee..hhhhhhhhhhhhh..eeeeeeeee.....hhhhhhh...hhh.eeeeee....eeee..eee......eeeee....hhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh........hhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wfi A   1 MKIAIAGAGAMGSRFGLMLHQSGNEVLLIDGWAEHVQQIKEHGLQANFNGKEVEAKLPIVLQSEVEKEDQVDLIILFTKAMQLEKMLQDIQSLIKKDTEVLCLLNGIGHEDIIEKFVPMENIYIGNTMWTAGLEGPGQVKLFGSGSVELQNLGDGKEAAAKKLADKLSESGLNAHFSDNIHYSIYRKACVNGTMNGLCTILDVNMAELGKTSTAHKMVATIVNEFAKVAAVEKIELDVPEVIAHCESCFDPETIGLHYPSMYQDLIKNHRLTEIDYINGAISRKGKKYGVATPYCDFLTELVHAKEDSLNV 311
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 


Chain B from PDB  Type:PROTEIN  Length:312
 aligned with E3USM3_ENTFC | E3USM3 from UniProtKB/TrEMBL  Length:312

    Alignment length:312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310  
         E3USM3_ENTFC     1 MKIAIAGAGAMGSRFGLMLHQSGNEVLLIDGWAEHVQQIKEHGLQANFNGKEVEAKLPIVLQSEVEKEDQVDLIILFTKAMQLEKMLQDIQSLIKKDTEVLCLLNGIGHEDIIEKFVPMENIYIGNTMWTAGLEGPGQVKLFGSGSVELQNLGDGKEAAAKKLADKLSESGLNAHFSDNIHYSIYRKACVNGTMNGLCTILDVNMAELGKTSTAHKMVATIVNEFAKVAAVEKIELDVPEVIAHCESCFDPETIGLHYPSMYQDLIKNHRLTEIDYINGAISRKGKKYGVATPYCDFLTELVHAKEDSLNVK 312
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhheeee....eeee...eee.........eeeeee..hhhhhhhhhhhhh..eeeeeeeee.....hhhhhhh...hhh.eeeeee....eeee..eee......eeeee....hhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh........hhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wfi B   1 MKIAIAGAGAMGSRFGLMLHQSGNEVLLIDGWAEHVQQIKEHGLQANFNGKEVEAKLPIVLQSEVEKEDQVDLIILFTKAMQLEKMLQDIQSLIKKDTEVLCLLNGIGHEDIIEKFVPMENIYIGNTMWTAGLEGPGQVKLFGSGSVELQNLGDGKEAAAKKLADKLSESGLNAHFSDNIHYSIYRKACVNGTMNGLCTILDVNMAELGKTSTAHKMVATIVNEFAKVAAVEKIELDVPEVIAHCESCFDPETIGLHYPSMYQDLIKNHRLTEIDYINGAISRKGKKYGVATPYCDFLTELVHAKEDSLNVK 312
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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  (0, 0)

(no "SCOP Domain" information available for 3WFI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WFI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WFI)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (E3USM3_ENTFC | E3USM3)
molecular function
    GO:0008677    2-dehydropantoate 2-reductase activity    Catalysis of the reaction: (R)-pantoate + NADP(+) = 2-dehydropantoate + H(+) + NADPH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0015940    pantothenate biosynthetic process    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid. It is a B complex vitamin that is a constituent of coenzyme A and is distributed ubiquitously in foods.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  Sites
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  Cis Peptide Bonds
    Asn A:49 - Gly A:50   [ RasMol ]  
    Asn B:49 - Gly B:50   [ RasMol ]  
 

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