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(-) Description

Title :  CRYSTAL STRUCTURE OF THE APO FORMS OF RHODOTORULA GRAMINIS D-MANDELATE DEHYDROGENASE AT 1.8A.
 
Authors :  S. G. Vachieri, A. R. Cole, C. Bagneris, D. P. Baker, C. A. Fewson, A. K. Basak
Date :  02 Nov 08  (Deposition) - 17 Nov 09  (Release) - 17 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mandelate Dehydrogenase, 2-Hydroxyacid Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. G. Vachieri, A. R. Cole, C. Bagneris, D. P. Baker, C. A. Fewson, A. K. Basak
Crystal Structure Of The Apo And Holo Forms Of Rhodotorula Graminis D(-)-Mandelate Dehydrogenase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-MANDELATE DEHYDROGENASE
    Chains: A
    Organism Scientific: RHODOTORULA GRAMINIS
    Organism Taxid: 29898
    Strain: KGX39
 
Molecule 2 - D-MANDELATE DEHYDROGENASE
    Chains: B
    Organism Scientific: RHODOTORULA GRAMINIS
    Organism Taxid: 29898
    Other Details: THE PROTEIN IS BIOLOGICALLY ACTIVE AND CRYSTALLIZES AS A DIMER
    Other Details - Source: C.A.FEWSON
    Strain: KGX39

 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 2W2K)

(-) Sites  (0, 0)

(no "Site" information available for 2W2K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W2K)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:67 -Pro A:68
2Glu A:286 -Pro A:287
3Tyr B:67 -Pro B:68
4Glu B:286 -Pro B:287

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W2K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W2K)

(-) Exons   (0, 0)

(no "Exon" information available for 2W2K)

(-) 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:345
 aligned with Q7LLW9_RHOGR | Q7LLW9 from UniProtKB/TrEMBL  Length:348

    Alignment length:345
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341     
         Q7LLW9_RHOGR     2 PRPRVLLLGDPARHLDDLWSDFQQKFEVIPANLTTHDGFKQALREKRYGDFEAIIKLAVENGTESYPWNADLISHLPSSLKVFAAAGAGFDWLDLDALNERGVAFANSRGAGDTATSDLALYLILSVFRLASYSERAARTGDPETFNRVHLEIGKSAHNPRGHVLGAVGLGAIQKEIARKAVHGLGMKLVYYDVAPADAETEKALGAERVDSLEELARRSDCVSVSVPYMKLTHHLIDEAFFAAMKPGSRIVNTARGPVISQDALIAALKSGKLLSAGLDVHEFEPQVSKELIEMKHVTLTTHIGGVAIETFHEFERLTMTNIDRFLLQGKPLLTPAGKVFAPSS 346
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------2w2kA02 A:114-309 NAD(P)-binding Rossmann-like Domain                                                                                                                                               ------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhheeee....hhhhhhhhhhh.......eeee.....hhhhh..hhhhhh.......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........eeeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhh.ee..hhhhhhhhh.eeee....hhhhh...hhhhhhhh...eeeee..hhhh.hhhhhhhhhhh..eeeeee.........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w2k A   2 PRPRVLLLGDPARHLDDLWSDFQQKFEVIPANLTTHDGFKQALREKRYGDFEAIIKLAVENGTESYPWNADLISHLPSSLKVFAAAGAGFDWLDLDALNERGVAFANSRGAGDTATSDLALYLILSVFRLASYSERAARTGDPETFNRVHLEIGKSAHNPRGHVLGAVGLGAIQKEIARKAVHGLGMKLVYYDVAPADAETEKALGAERVDSLEELARRSDCVSVSVPYMKLTHHLIDEAFFAAMKPGSRIVNTARGPVISQDALIAALKSGKLLSAGLDVHEFEPQVSKELIEMKHVTLTTHIGGVAIETFHEFERLTMTNIDRFLLQGKPLLTPAGKVFAPSS 346
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341     


Chain B from PDB  Type:PROTEIN  Length:344
 aligned with Q7LLW9_RHOGR | Q7LLW9 from UniProtKB/TrEMBL  Length:348

    Alignment length:344
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341    
         Q7LLW9_RHOGR     2 PRPRVLLLGDPARHLDDLWSDFQQKFEVIPANLTTHDGFKQALREKRYGDFEAIIKLAVENGTESYPWNADLISHLPSSLKVFAAAGAGFDWLDLDALNERGVAFANSRGAGDTATSDLALYLILSVFRLASYSERAARTGDPETFNRVHLEIGKSAHNPRGHVLGAVGLGAIQKEIARKAVHGLGMKLVYYDVAPADAETEKALGAERVDSLEELARRSDCVSVSVPYMKLTHHLIDEAFFAAMKPGSRIVNTARGPVISQDALIAALKSGKLLSAGLDVHEFEPQVSKELIEMKHVTLTTHIGGVAIETFHEFERLTMTNIDRFLLQGKPLLTPAGKVFAPS 345
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------2w2kB02 B:114-309 NAD(P)-binding Rossmann-like Domain                                                                                                                                               ------------------------------------ CATH domains
           Pfam domains (1) ---------------2-Hacid_dh-2w2kB01 B:17-336                                                                                                                                                                                                                                                                                                     --------- Pfam domains (1)
           Pfam domains (2) ---------------2-Hacid_dh-2w2kB02 B:17-336                                                                                                                                                                                                                                                                                                     --------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------2-Hacid_dh_C-2w2kB03 B:122-306                                                                                                                                                           --------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------2-Hacid_dh_C-2w2kB04 B:122-306                                                                                                                                                           --------------------------------------- Pfam domains (4)
         Sec.struct. author ...eeee.......hhhhhhhhhhhheeee....hhhhhhhhhhh.......eeee.....hhhhh..hhhhhh.......eeee........hhhhhhhh..eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.........eeeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhh.ee..hhhhhhhhh.eeee....hhhhh...hhhhhhhh...eeeee..hhhh.hhhhhhhhhhh..eeeeee.........hhhhhh...eee.......hhhhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w2k B   2 PRPRVLLLGDPARHLDDLWSDFQQKFEVIPANLTTHDGFKQALREKRYGDFEAIIKLAVENGTESYPWNADLISHLPSSLKVFAAAGAGFDWLDLDALNERGVAFANSRGAGDTATSDLALYLILSVFRLASYSERAARTGDPETFNRVHLEIGKSAHNPRGHVLGAVGLGAIQKEIARKAVHGLGMKLVYYDVAPADAETEKALGAERVDSLEELARRSDCVSVSVPYMKLTHHLIDEAFFAAMKPGSRIVNTARGPVISQDALIAALKSGKLLSAGLDVHEFEPNVSKELIEMKHVTLTTHIGGVAIETFHEFERLTMTNIDRFLLQGKPLLTPAGKVFAPS 345
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341
   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 2W2K)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Form_Glyc_dh (56)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7LLW9_RHOGR | Q7LLW9)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    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.
    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.

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  Cis Peptide Bonds
    Glu A:286 - Pro A:287   [ RasMol ]  
    Glu B:286 - Pro B:287   [ RasMol ]  
    Tyr A:67 - Pro A:68   [ RasMol ]  
    Tyr B:67 - Pro B:68   [ RasMol ]  
 

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 Related Entries

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        Q7LLW9_RHOGR | Q7LLW9: 2w2l

(-) Related Entries Specified in the PDB File

2w2l CRYSTAL STRUCTURE OF THE HOLO FORMS OF RHODOTORULA GRAMINIS D-MANDELATE DEHYDROGENASE AT 2.5A.