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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TERNARY COMPLEX OF AN ISOMERASE
 
Authors :  T. Umeda, N. Tanaka, Y. Kusakabe, M. Nakanishi, Y. Kitade, K. T. Nakamur
Date :  01 Feb 11  (Deposition) - 10 Aug 11  (Release) - 12 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nadph Binding, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Umeda, N. Tanaka, Y. Kusakabe, M. Nakanishi, Y. Kitade, K. T. Nakamura
Molecular Basis Of Fosmidomycin'S Action On The Human Malaria Parasite Plasmodium Falciparum
Sci Rep V. 1 9 2011
PubMed-ID: 22355528  |  Reference-DOI: 10.1038/SREP00009

(-) Compounds

Molecule 1 - 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DXR
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:84 , THR A:86 , GLY A:87 , SER A:88 , ILE A:89 , TYR A:113 , VAL A:114 , ASN A:115 , LYS A:116 , SER A:117 , HIS A:136 , GLY A:180 , ILE A:181 , ASP A:182 , GLN A:185 , ALA A:203 , ASN A:204 , LYS A:205 , GLU A:206 , ASP A:231 , MET A:360 , HOH A:513 , HOH A:524 , HOH A:532 , HOH A:661BINDING SITE FOR RESIDUE NDP A 501
2AC2SOFTWAREASP A:231 , GLU A:233 , GLU A:315 , HOH A:539 , HOH A:660 , HOH A:665BINDING SITE FOR RESIDUE MN A 601
3AC3SOFTWAREGLY B:84 , THR B:86 , GLY B:87 , SER B:88 , ILE B:89 , TYR B:113 , VAL B:114 , ASN B:115 , LYS B:116 , SER B:117 , HIS B:136 , GLY B:180 , ILE B:181 , ASP B:182 , GLN B:185 , ALA B:203 , ASN B:204 , LYS B:205 , ASP B:231 , HOH B:505 , HOH B:534 , HOH B:567BINDING SITE FOR RESIDUE NDP B 502
4AC4SOFTWAREASP B:231 , GLU B:233 , GLU B:315 , HOH B:509 , HOH B:665 , HOH B:671BINDING SITE FOR RESIDUE MN B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3AU8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Trp A:370 -Pro A:371
2Trp B:370 -Pro B:371

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3AU8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3AU8)

(-) Exons   (0, 0)

(no "Exon" information available for 3AU8)

(-) 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:399
 aligned with DXR_PLAFX | O96693 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:408
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476        
            DXR_PLAFX    77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNK 484
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh.....eeeehhhhhhhhhhh....eeee..hhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh.......hhhhhh.eeeeeeee........hhhhhh.......---------hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3au8 A  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENA---------KKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNK 484
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286   |     -   |   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476        
                                                                                                                                                                                                                                               290       300                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:405
 aligned with DXR_PLAFX | O96693 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:408
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476        
            DXR_PLAFX    77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNK 484
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh..eeee.hhhhhhhhhhhhh.......eeeehhhhhhhhhhh....eeee...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhh.......hhhhhh.eeeeeeee........hhhhhhhhhhhhhhhh...---hhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee.....eeeeeee....eeeee....hhhhhhhhhhh...........hhhhhheee........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3au8 B  77 PINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKW---KKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNK 484
                                    86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296   |   306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476        
                                                                                                                                                                                                                                                     296 300
   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 3AU8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3AU8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3AU8)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DXR_PLAFX | O96693)
molecular function
    GO:0030604    1-deoxy-D-xylulose-5-phosphate reductoisomerase activity    Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + H(+) + NADPH.
    GO:0070402    NADPH binding    Interacting selectively and non-covalently with the reduced form, NADPH, of nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019288    isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway    The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    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:0020011    apicoplast    The plastid organelle found in apicomplexans.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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  3au8
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DXR_PLAFX | O96693: 3au9 3aua 3wqq 3wqr 3wqs 4gae 4kp7

(-) Related Entries Specified in the PDB File

3au9 3aua