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(-) Description

Title :  RICE KETOLACID REDUCTOISOMERASE IN COMPLEX WITH MG2+-NADPH
 
Authors :  E. W. W. Leung, L. W. Guddat
Date :  08 Jan 09  (Deposition) - 14 Apr 09  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Branched-Chain Amino Acid Biosynthesis, Knotted Protein, Nadph, Isomerase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. W. Leung, L. W. Guddat
Conformational Changes In A Plant Ketol-Acid Reductoisomerase Upon Mg(2+) And Nadph Binding As Revealed By Two Crystal Structures
J. Mol. Biol. V. 389 167 2009
PubMed-ID: 19362563  |  Reference-DOI: 10.1016/J.JMB.2009.04.012

(-) Compounds

Molecule 1 - PUTATIVE KETOL-ACID REDUCTOISOMERASE (OS05G0573700 PROTEIN)
    Chains: A, B
    EC Number: 1.1.1.86
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30(A)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 54-578
    Gene: ILVB, OJ1735_C10.18, OS05G0573700
    Organism Common: JAPANESE RICE
    Organism Scientific: ORYZA SATIVA JAPONICA GROUP
    Organism Taxid: 39947

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
3PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5SO41Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:315 , GLU A:492 , GLU A:496 , HOH A:663 , PE4 A:6061BINDING SITE FOR RESIDUE MG A 1
2AC2SOFTWAREARG A:337 , TYR A:338 , GLN A:341 , HIS A:461 , PHE A:463BINDING SITE FOR RESIDUE SO4 A 597
3AC3SOFTWARETRP A:133 , GLY A:134 , SER A:135 , GLN A:136 , ARG A:162 , SER A:165 , SER A:167 , LEU A:199 , ILE A:200 , SER A:201 , ASP A:202 , ALA A:204 , GLN A:205 , ASN A:208 , SER A:225 , HIS A:226 , GLY A:253 , MET A:254 , SER A:518 , PE4 A:6061BINDING SITE FOR RESIDUE NDP A 601
4AC4SOFTWAREMG A:1 , ASP A:315 , GLU A:319 , GLU A:496 , CYS A:517 , SER A:518 , NDP A:601 , HOH A:663BINDING SITE FOR RESIDUE PE4 A6061
5AC5SOFTWAREHIS B:226 , ASP B:315 , GLU B:319 , HOH B:667 , PEG B:6073BINDING SITE FOR RESIDUE MG B 1
6AC6SOFTWAREASP B:315 , GLU B:496 , HOH B:670 , PEG B:6073BINDING SITE FOR RESIDUE MG B 597
7AC7SOFTWARETRP B:133 , GLY B:134 , SER B:135 , GLN B:136 , ARG B:162 , SER B:165 , SER B:167 , LEU B:199 , ILE B:200 , SER B:201 , ASP B:202 , ALA B:204 , GLN B:205 , ASN B:208 , SER B:225 , HIS B:226 , PRO B:251 , GLY B:253 , MET B:254 , GLY B:255 , SER B:518 , THR B:519 , ARG B:589 , PEG B:6073BINDING SITE FOR RESIDUE NDP B 600
8AC8SOFTWAREMG B:1 , ASP B:315 , GLU B:319 , GLU B:496 , SER B:518 , MG B:597 , NDP B:600BINDING SITE FOR RESIDUE PEG B6073

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3FR8)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro B:77 -Ala B:78
2Leu B:148 -Ala B:149
3Asp B:169 -Glu B:170

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3FR8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3FR8)

(-) Exons   (0, 0)

(no "Exon" information available for 3FR8)

(-) 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:501
 aligned with ILV5_ORYSJ | Q65XK0 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:501
                                    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       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562 
           ILV5_ORYSJ    63 AAMPSLDFDTSVFNKEKVSLAGHEEYIVRGGRNLFPLLPEAFKGIKQIGVIGWGSQGPAQAQNLRDSLAEAKSDIVVKIGLRKGSKSFDEARAAGFTEESGTLGDIWETVSGSDLVLLLISDAAQADNYEKIFSHMKPNSILGLSHGFLLGHLQSAGLDFPKNISVIAVCPKGMGPSVRRLYVQGKEINGAGINSSFAVHQDVDGRATDVALGWSVALGSPFTFATTLEQEYKSDIFGERGILLGAVHGIVEALFRRYTEQGMDEEMAYKNTVEGITGIISKTISKKGMLEVYNSLTEEGKKEFNKAYSASFYPCMDILYECYEDVASGSEIRSVVLAGRRFYEKEGLPAFPMGNIDQTRMWKVGEKVRSTRPENDLGPLHPFTAGVYVALMMAQIEVLRKKGHSYSEIINESVIESVDSLNPFMHARGVAFMVDNCSTTARLGSRKWAPRFDYILTQQAFVTVDKDAPINQDLISNFMSDPVHGAIEVCAELRPTVDISV 563
               SCOP domains d3fr8a1 A:81-307 automated matches                                                                                                                                                                                                 d3fr8a2 A:308-581 automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeee..eeeeeee.hhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.........eeeeee.....hhhhhhh.........eeehhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee..hhhhhhhhh.........eeeeeee..hhhhhhhhhhhh.........eeeeeee....hhhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fr8 A  81 AAMPSLDFDTSVFNKEKVSLAGHEEYIVRGGRNLFPLLPEAFKGIKQIGVIGWGSQGPAQAQNLRDSLAEAKSDIVVKIGLRKGSKSFDEARAAGFTEESGTLGDIWETVSGSDLVLLLISDAAQADNYEKIFSHMKPNSILGLSHGFLLGHLQSAGLDFPKNISVIAVCPKGMGPSVRRLYVQGKEINGAGINSSFAVHQDVDGRATDVALGWSVALGSPFTFATTLEQEYKSDIFGERGILLGAVHGIVEALFRRYTEQGMDEEMAYKNTVEGITGIISKTISKKGMLEVYNSLTEEGKKEFNKAYSASFYPCMDILYECYEDVASGSEIRSVVLAGRRFYEKEGLPAFPMGNIDQTRMWKVGEKVRSTRPENDLGPLHPFTAGVYVALMMAQIEVLRKKGHSYSEIINESVIESVDSLNPFMHARGVAFMVDNCSTTARLGSRKWAPRFDYILTQQAFVTVDKDAPINQDLISNFMSDPVHGAIEVCAELRPTVDISV 581
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580 


Chain B from PDB  Type:PROTEIN  Length:517
 aligned with ILV5_ORYSJ | Q65XK0 from UniProtKB/Swiss-Prot  Length:578

    Alignment length:517
                                    68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       
           ILV5_ORYSJ    59 PAVGAAMPSLDFDTSVFNKEKVSLAGHEEYIVRGGRNLFPLLPEAFKGIKQIGVIGWGSQGPAQAQNLRDSLAEAKSDIVVKIGLRKGSKSFDEARAAGFTEESGTLGDIWETVSGSDLVLLLISDAAQADNYEKIFSHMKPNSILGLSHGFLLGHLQSAGLDFPKNISVIAVCPKGMGPSVRRLYVQGKEINGAGINSSFAVHQDVDGRATDVALGWSVALGSPFTFATTLEQEYKSDIFGERGILLGAVHGIVEALFRRYTEQGMDEEMAYKNTVEGITGIISKTISKKGMLEVYNSLTEEGKKEFNKAYSASFYPCMDILYECYEDVASGSEIRSVVLAGRRFYEKEGLPAFPMGNIDQTRMWKVGEKVRSTRPENDLGPLHPFTAGVYVALMMAQIEVLRKKGHSYSEIINESVIESVDSLNPFMHARGVAFMVDNCSTTARLGSRKWAPRFDYILTQQAFVTVDKDAPINQDLISNFMSDPVHGAIEVCAELRPTVDISVPANADFVRPELR 575
               SCOP domains d3fr8b1 B:77-307 automated matches                                                                                                                                                                                                     d3fr8b2 B:308-593 automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................eeeee..eeeeeee.hhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.........eeeeee........hhhhhh.......eeehhhhhhh..eeee..hhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh........eeeeeee..hhhhhhhh.hhhhhh......eeeeeee....hhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhh...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fr8 B  77 PAVGAAMPSLDFDTSVFNKEKVSLAGHEEYIVRGGRNLFPLLPEAFKGIKQIGVIGWGSQGPAQAQNLRDSLAEAKSDIVVKIGLRKGSKSFDEARAAGFTEESGTLGDIWETVSGSDLVLLLISDAAQADNYEKIFSHMKPNSILGLSHGFLLGHLQSAGLDFPKNISVIAVCPKGMGPSVRRLYVQGKEINGAGINSSFAVHQDVDGRATDVALGWSVALGSPFTFATTLEQEYKSDIFGERGILLGAVHGIVEALFRRYTEQGMDEEMAYKNTVEGITGIISKTISKKGMLEVYNSLTEEGKKEFNKAYSASFYPCMDILYECYEDVASGSEIRSVVLAGRRFYEKEGLPAFPMGNIDQTRMWKVGEKVRSTRPENDLGPLHPFTAGVYVALMMAQIEVLRKKGHSYSEIINESVIESVDSLNPFMHARGVAFMVDNCSTTARLGSRKWAPRFDYILTQQAFVTVDKDAPINQDLISNFMSDPVHGAIEVCAELRPTVDISVPANADFVRPELR 593
                                    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       486       496       506       516       526       536       546       556       566       576       586
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3FR8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3FR8)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ILV5_ORYSJ | Q65XK0)
molecular function
    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:0004455    ketol-acid reductoisomerase activity    Catalysis of the reaction: (R)-2,3-dihydroxy-3-methylbutanoate + NADP+ = (S)-2-hydroxy-2-methyl-3-oxobutanoate + NADPH + H+.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0009082    branched-chain amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009097    isoleucine biosynthetic process    The chemical reactions and pathways resulting in the formation of isoleucine, (2R*,3R*)-2-amino-3-methylpentanoic acid.
    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:0009099    valine biosynthetic process    The chemical reactions and pathways resulting in the formation of valine, 2-amino-3-methylbutanoic acid.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        ILV5_ORYSJ | Q65XK0: 3fr7

(-) Related Entries Specified in the PDB File

1qmg CRYSTAL STRUCTURE OF SPINACH ACETOHYDROXYACID ISOMEROREDUCTASE COMPLEXED WITH ITS REACTION PRODUCT DIHYDROXYMETHYLVALERATE, MANGANESE AND (PHOSPHO)-ADP-RIBOSE
1yrl CRYSTAL STRUCTURE OF FREE E. COLI KARI
1yve MG2+-NADPH-IPOHA BOUND KARI STRUCTURE FROM SPINACH
3fr7