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(-) Description

Title :  CRYSTAL STRUCTURE OF SHIKIMATE DEHYDROGENASE (AROE) FROM HAEMOPHILUS INFLUENZAE
 
Authors :  S. Ye, F. Von Delft, A. Brooun, M. W. Knuth, R. V. Swanson, D. E. Mcree
Date :  30 Apr 03  (Deposition) - 12 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Shikimate Dehydrogenase, Haemophilus Influenzae, Nadph, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ye, F. Von Delft, A. Brooun, M. W. Knuth, R. V. Swanson, D. E. Mcree
The Crystal Structure Of Shikimate Dehydrogenase (Aroe) Reveals A Unique Nadph Binding Mode
J. Bacteriol. V. 185 4144 2003
PubMed-ID: 12837789  |  Reference-DOI: 10.1128/JB.185.14.4144-4151.2003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SHIKIMATE 5-DEHYDROGENASE
    Chains: A
    EC Number: 1.1.1.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSX12
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: SHIKIMATE DEHYDROGENASE
    Gene: AROE OR HI0655
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ATR1Ligand/Ion2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:1 , LYS A:89 , PRO A:177 , GLN A:179 , TRP A:253 , ARG A:254 , GLY A:255 , HOH A:415BINDING SITE FOR RESIDUE ACT A 301
2AC2SOFTWAREGLY A:126 , ALA A:127 , GLY A:128 , GLY A:129 , ALA A:130 , ASN A:149 , ARG A:150 , THR A:151 , LYS A:154 , THR A:188 , SER A:189 , ALA A:190 , HOH A:348 , HOH A:361 , HOH A:445 , HOH A:450 , HOH A:485 , HOH A:516 , HOH A:535BINDING SITE FOR RESIDUE ATR A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P77)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:9 -Pro A:10
2Ser A:62 -Pro A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P77)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P77)

(-) Exons   (0, 0)

(no "Exon" information available for 1P77)

(-) 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:265
 aligned with AROE_HAEIN | P43876 from UniProtKB/Swiss-Prot  Length:272

    Alignment length:272
                                    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  
           AROE_HAEIN     1 MDLYAVWGNPIAQSKSPLIQNKLAAQTHQTMEYIAKLGDLDAFEQQLLAFFEEGAKGCNITSPFKERAYQLADEYSQRAKLAEACNTLKKLDDGKLYADNTDGIGLVTDLQRLNWLRPNQHVLILGAGGATKGVLLPLLQAQQNIVLANRTFSKTKELAERFQPYGNIQAVSMDSIPLQTYDLVINATSAGLSGGTASVDAEILKLGSAFYDMQYAKGTDTPFIALCKSLGLTNVSDGFGMLVAQAAHSFHLWRGVMPDFVSVYEQLKKAML 272
               SCOP domains d1p77a2 A:1-101 Shikimate 5-dehydrogenase AroE                                                       d1p77a1 A:102-272 Shikimate 5-dehydrogenase AroE                                                                                                                            SCOP domains
               CATH domains 1p77A01 A:1-114,A:238-272 Leucine Dehydrogenase, chain A, domain 1                                                1p77A02 A:115-237 NAD(P)-binding Rossmann-like Domain                                                                      1p77A01 A:1-114,A:238-272           CATH domains
               Pfam domains -----Shikimate_dh_N-1p77A02 A:6-88                                                      ---------------------Shikimate_DH-1p77A01 A:110-217                                                                              ------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh...eeee...hhhhhhhhh.eehhhhhhhh...eeee.....eeee.hhhhhhhhhhhhh.......eeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh.eeeee.hhh......eeee....-------..hhhhhhhh..eee........hhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p77 A   1 MDLYAVWGNPIAQSKSPLIQNKLAAQTHQTMEYIAKLGDLDAFEQQLLAFFEEGAKGCNITSPFKERAYQLADEYSQRAKLAEACNTLKKLDDGKLYADNTDGIGLVTDLQRLNWLRPNQHVLILGAGGATKGVLLPLLQAQQNIVLANRTFSKTKELAERFQPYGNIQAVSMDSIPLQTYDLVINATSA-------SVDAEILKLGSAFYDMQYAKGTDTPFIALCKSLGLTNVSDGFGMLVAQAAHSFHLWRGVMPDFVSVYEQLKKAML 272
                                    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  
                                                                                                                                                                                                                       190     198
   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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)
(-)
Clan: no clan defined [family: Shikimate_dh_N] (15)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AROE_HAEIN | P43876)
molecular function
    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.
    GO:0004764    shikimate 3-dehydrogenase (NADP+) activity    Catalysis of the reaction: shikimate + NADP+ = 3-dehydroshikimate + NADPH + H+.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    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:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.
    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:0019632    shikimate metabolic process    The chemical reactions and pathways involving shikimate, (3R,4S,5R)--3,4,5-trihydroxycyclohex-1-ene-1-carboxylate, the anion of shikimic acid. It is an important intermediate in the biosynthesis of aromatic amino acids.

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  1p77
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 Related Entries

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

UniProtKB/Swiss-Prot
        AROE_HAEIN | P43876: 1p74

(-) Related Entries Specified in the PDB File

1p74