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(-) Description

Title :  INITIAL STRUCTURAL ANALYSIS OF PLASMODIUM FALCIPARUM GLYCEROL-3-PHOSPHATE DEHYDROGENASE
 
Authors :  M. A. Robien, W. G. J. Hol, Structural Genomics Of Pathogenic Proto Consortium (Sgpp)
Date :  13 Jan 05  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Sgpp, Structural Genomics, Psi, Protein Structure Initiative, Structural Genomics Of Pathogenic Protozoa Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Robien, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa (Sgpp)
Initial Structural Analysis Of Plasmodium Falciparum Glycerol-3-Phosphate Dehydrogenase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCEROL-3-PHOSPHATE DEHYDROGENASE
    Chains: A, B, C
    EC Number: 1.1.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21STAR/DE3
    Expression System Taxid: 562
    Expression System Vector Type: T7 SYSTEM
    Gene: PFL0780W
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1YJ8)

(-) Sites  (0, 0)

(no "Site" information available for 1YJ8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YJ8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YJ8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YJ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1YJ8)

(-) Exons   (0, 0)

(no "Exon" information available for 1YJ8)

(-) 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 Q8I5P5_PLAF7 | Q8I5P5 from UniProtKB/TrEMBL  Length:367

    Alignment length:363
                                    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       351       361   
         Q8I5P5_PLAF7     2 YRNLFDKLKDGPLKISILGSGNWASAISKVVGTNAKNNYLFENEVRMWIRDEFVNGERMVDIINNKHENTKYLKGVPLPHNIVAHSDLASVINDADLLIFIVPCQYLESVLASIKESESIKIASHAKAISLTKGFIVKKNQMKLCSNYISDFLNIPCSALSGANIAMDVAMENFSEATIGGNDKDSLVIWQRVFDLPYFKINCVNETIEVEICGALKNIITLACGFCDGLNLPTNSKSAIIRNGINEMILFGKVFFQKFNENILLESCGFADIITSFLAGRNAKCSAEFIKSTPKKTWEELENEILKGQKLQGTVTLKYVYHMIKEKNMTNEFPLFTVLHKISFENEDPSSLLKTFMNNKINQ 364
               SCOP domains d1yj8a1 A:10-215 automated matches                                                                                                                                                                            d1yj8a2 A:216-372 automated matches                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhh......eeee.....---.hhhhhhhhhh..............eeee..hhhhhh...eeee..hhhhhhhhhhhhh.---.......eeee.....eee..eeehhhhhhhhhh...eeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj8 A  10 YRNLFDKLKDGPLKISILGSGNWASAISKVVGTNAKNNYLFENEVRMWIRDEF---ERMVDIINNKHENTKYLKGVPLPHNIVAHSDLASVINDADLLIFIVPCQYLESVLASIKE---IKIASHAKAISLTKGFIVKKNQMKLCSNYISDFLNIPCSALSGANIAMDVAMENFSEATIGGNDKDSLVIWQRVFDLPYFKINCVNETIEVEICGALKNIITLACGFCDGLNLPTNSKSAIIRNGINEMILFGKVFFQKFNENILLESCGFADIITSFLAGRNAKCSAEFIKSTPKKTWEELENEILKGQKLQGTVTLKYVYHMIKEKNMTNEFPLFTVLHKISFENEDPSSLLKTFMNNKINQ 372
                                    19        29        39        49        59  |   | 69        79        89        99       109       119     | 129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369   
                                                                               62  66                                                        125 129                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:357
 aligned with Q8I5P5_PLAF7 | Q8I5P5 from UniProtKB/TrEMBL  Length:367

    Alignment length:363
                                    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       351       361   
         Q8I5P5_PLAF7     2 YRNLFDKLKDGPLKISILGSGNWASAISKVVGTNAKNNYLFENEVRMWIRDEFVNGERMVDIINNKHENTKYLKGVPLPHNIVAHSDLASVINDADLLIFIVPCQYLESVLASIKESESIKIASHAKAISLTKGFIVKKNQMKLCSNYISDFLNIPCSALSGANIAMDVAMENFSEATIGGNDKDSLVIWQRVFDLPYFKINCVNETIEVEICGALKNIITLACGFCDGLNLPTNSKSAIIRNGINEMILFGKVFFQKFNENILLESCGFADIITSFLAGRNAKCSAEFIKSTPKKTWEELENEILKGQKLQGTVTLKYVYHMIKEKNMTNEFPLFTVLHKISFENEDPSSLLKTFMNNKINQ 364
               SCOP domains d1yj8b1 B:10-215 automated matches                                                                                                                                                                            d1yj8b2 B:216-372 automated matches                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhh......eeee.....---.hhhhhhhhhh..............eeee..hhhhhh...eeee..hhhhhhhhhhhhh.---.......eeee.....eee..eeehhhhhhhhhh...eeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj8 B  10 YRNLFDKLKDGPLKISILGSGNWASAISKVVGTNAKNNYLFENEVRMWIRDEF---ERMVDIINNKHENTKYLKGVPLPHNIVAHSDLASVINDADLLIFIVPCQYLESVLASIKE---IKIASHAKAISLTKGFIVKKNQMKLCSNYISDFLNIPCSALSGANIAMDVAMENFSEATIGGNDKDSLVIWQRVFDLPYFKINCVNETIEVEICGALKNIITLACGFCDGLNLPTNSKSAIIRNGINEMILFGKVFFQKFNENILLESCGFADIITSFLAGRNAKCSAEFIKSTPKKTWEELENEILKGQKLQGTVTLKYVYHMIKEKNMTNEFPLFTVLHKISFENEDPSSLLKTFMNNKINQ 372
                                    19        29        39        49        59  |   | 69        79        89        99       109       119     | 129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369   
                                                                               62  66                                                        125 129                                                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:357
 aligned with Q8I5P5_PLAF7 | Q8I5P5 from UniProtKB/TrEMBL  Length:367

    Alignment length:363
                                    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       351       361   
         Q8I5P5_PLAF7     2 YRNLFDKLKDGPLKISILGSGNWASAISKVVGTNAKNNYLFENEVRMWIRDEFVNGERMVDIINNKHENTKYLKGVPLPHNIVAHSDLASVINDADLLIFIVPCQYLESVLASIKESESIKIASHAKAISLTKGFIVKKNQMKLCSNYISDFLNIPCSALSGANIAMDVAMENFSEATIGGNDKDSLVIWQRVFDLPYFKINCVNETIEVEICGALKNIITLACGFCDGLNLPTNSKSAIIRNGINEMILFGKVFFQKFNENILLESCGFADIITSFLAGRNAKCSAEFIKSTPKKTWEELENEILKGQKLQGTVTLKYVYHMIKEKNMTNEFPLFTVLHKISFENEDPSSLLKTFMNNKINQ 364
               SCOP domains d1yj8c1 C:10-215 automated matches                                                                                                                                                                            d1yj8c2 C:216-372 automated matches                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------NAD_Gly3P_dh_N-1yj8C04 C:23-196                                                                                                                                               -----------------NAD_Gly3P_dh_C-1yj8C01 C:214-365                                                                                                                        ------- Pfam domains (1)
           Pfam domains (2) -------------NAD_Gly3P_dh_N-1yj8C05 C:23-196                                                                                                                                               -----------------NAD_Gly3P_dh_C-1yj8C02 C:214-365                                                                                                                        ------- Pfam domains (2)
           Pfam domains (3) -------------NAD_Gly3P_dh_N-1yj8C06 C:23-196                                                                                                                                               -----------------NAD_Gly3P_dh_C-1yj8C03 C:214-365                                                                                                                        ------- Pfam domains (3)
         Sec.struct. author ..hhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhh......eeee.....---.hhhhhhhhhh..............eeee..hhhhhh...eeee..hhhhhhhhhhhhh.---.......eeee.....eee..eeehhhhhhhhhh...eeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhh..hhhhhhhhhhh....hhhhhhhhh.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh....hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yj8 C  10 YRNLFDKLKDGPLKISILGSGNWASAISKVVGTNAKNNYLFENEVRMWIRDEF---ERMVDIINNKHENTKYLKGVPLPHNIVAHSDLASVINDADLLIFIVPCQYLESVLASIKE---IKIASHAKAISLTKGFIVKKNQMKLCSNYISDFLNIPCSALSGANIAMDVAMENFSEATIGGNDKDSLVIWQRVFDLPYFKINCVNETIEVEICGALKNIITLACGFCDGLNLPTNSKSAIIRNGINEMILFGKVFFQKFNENILLESCGFADIITSFLAGRNAKCSAEFIKSTPKKTWEELENEILKGQKLQGTVTLKYVYHMIKEKNMTNEFPLFTVLHKISFENEDPSSLLKTFMNNKINQ 372
                                    19        29        39        49        59  |   | 69        79        89        99       109       119     | 129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369   
                                                                               62  66                                                        125 129
   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, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1YJ8)

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: 6PGD_C (47)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8I5P5_PLAF7 | Q8I5P5)
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:0004367    glycerol-3-phosphate dehydrogenase [NAD+] activity    Catalysis of the reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH + H+.
    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.
    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.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0046168    glycerol-3-phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of glycerol-3-phosphate, a phosphoric monoester of glycerol.
    GO:0006072    glycerol-3-phosphate metabolic process    The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
    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.
cellular component
    GO:0009331    glycerol-3-phosphate dehydrogenase complex    An enzyme complex that catalyzes the dehydrogenation of sn-glycerol 3-phosphate to form glycerone phosphate.

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