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(-) Description

Title :  CRYSTAL STRUCTURE OF KETOPANTOATE REDUCTASE IN COMPLEX WITH NADP+
 
Authors :  C. M. C. Lobley, A. Ciulli, H. M. Whitney, G. Williams, A. G. Smith, C. Abell, T. L. Blundell
Date :  15 Jan 05  (Deposition) - 28 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A
Keywords :  Ketopantoate, Nadp+ Dependent, Pantothenate Pathway, Secondary Alcohol Dehydrogenase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Lobley, A. Ciulli, H. M. Whitney, G. Williams, A. G. Smith, C. Abell, T. L. Blundell
The Crystal Structure Of Escherichia Coli Ketopantoate Reductase With Nadp+ Bound.
Biochemistry V. 44 8930 2005
PubMed-ID: 15966718  |  Reference-DOI: 10.1021/BI0502036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2-DEHYDROPANTOATE 2-REDUCTASE
    Chains: A
    EC Number: 1.1.1.169
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PANE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: KETOPANTOATE REDUCTASE, KPA REDUCTASE, KPR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:738BINDING SITE FOR RESIDUE ACT A 701
2AC2SOFTWAREASP A:148BINDING SITE FOR RESIDUE ACT A 702
3AC3SOFTWAREGLY A:7 , GLY A:9 , ALA A:10 , LEU A:11 , TRP A:29 , LEU A:30 , ARG A:31 , LEU A:71 , LYS A:72 , GLN A:75 , ALA A:79 , HIS A:97 , ASN A:98 , THR A:118 , HIS A:120 , ALA A:121 , ALA A:122 , GLU A:256 , HOH A:715 , HOH A:754 , HOH A:779 , HOH A:807 , HOH A:831 , HOH A:838 , HOH A:854 , HOH A:900 , HOH A:917BINDING SITE FOR RESIDUE NAP A 501
4AC4SOFTWARECYS A:20 , GLY A:23 , GLU A:203 , GLU A:277 , HOH A:714BINDING SITE FOR RESIDUE MPD A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:161 -Asp A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YJQ)

(-) 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:293
 aligned with PANE_ECOLI | P0A9J4 from UniProtKB/Swiss-Prot  Length:303

    Alignment length:293
                                    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   
           PANE_ECOLI     1 MKITVLGCGALGQLWLTALCKQGHEVQGWLRVPQPYCSVNLVETDGSIFNESLTANDPDFLATSDLLLVTLKAWQVSDAVKSLASTLPVTTPILLIHNGMGTIEELQNIQQPLLMGTTTHAARRDGNVIIHVANGITHIGPARQQDGDYSYLADILQTVLPDVAWHNNIRAELWRKLAVNCVINPLTAIWNCPNGELRHHPQEIMQICEEVAAVIEREGHHTSAEDLRDYVMQVIDATAENISSMLQDIRALRHTEIDYINGFLLRRARAHGIAVPENTRLFEMVKRKESEYE 293
               SCOP domains d1yjqa2 A:1-167 Ketopantoate reductase PanE                                                                                                                            d1yjqa1 A:168-293 Ketopantoate reductase PanE                                                                                  SCOP domains
               CATH domains 1yjqA01 A:1-167 NAD(P)-binding Rossmann-like Domain                                                                                                                    1yjqA02 A:168-290 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                --- CATH domains
               Pfam domains --ApbA-1yjqA01 A:3-144                                                                                                                          -----------------------ApbA_C-1yjqA02 A:168-289                                                                                                  ---- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee......eeeeeee.....eeeeeee..hhhhhh...eeee..hhhhhhhhhhhhh........eeee.....hhhhhh.....eeeeee..eeeee..eeeeee...eeeee.......hhhhhhhhhh....eee..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yjq A   1 MKITVLGCGALGQLWLTALCKQGHEVQGWLRVPQPYCSVNLVETDGSIFNESLTANDPDFLATSDLLLVTLKAWQVSDAVKSLASTLPVTTPILLIHNGMGTIEELQNIQQPLLMGTTTHAARRDGNVIIHVANGITHIGPARQQDGDYSYLADILQTVLPDVAWHNNIRAELWRKLAVNCVINPLTAIWNCPNGELRHHPQEIMQICEEVAAVIEREGHHTSAEDLRDYVMQVIDATAENISSMLQDIRALRHTEIDYINGFLLRRARAHGIAVPENTRLFEMVKRKESEYE 293
                                    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
   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, 2)

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

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: ApbA_C] (5)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PANE_ECOLI | P0A9J4)
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: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.
    GO:0033317    pantothenate biosynthetic process from valine    The chemical reactions and pathways resulting in the formation of pantothenate, the anion of pantothenic acid, from other compounds, including valine.
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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  1yjq
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 Related Entries

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

UniProtKB/Swiss-Prot
        PANE_ECOLI | P0A9J4: 1ks9 1yon 2ofp

(-) Related Entries Specified in the PDB File

1ks9 APO VERSION OF THE SAME PROTEIN