The Open Protein Structure Annotation Network
PDB Keyword


    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary

    Title Crystal structure of Homoserine dehydrogenase (NP_394635.1) from THERMOPLASMA ACIDOPHILUM at 1.95 A resolution. To be published
    Site JCSG
    PDB Id 3ing Target Id 380082
    Molecular Characteristics
    Source Thermoplasma acidophilum dsm 1728
    Alias Ids TPS20823,NP_394635.1, 87211 Molecular Weight 35603.14 Da.
    Residues 324 Isoelectric Point 5.44
    Sequence mkeiriilmgtgnvglnvlriidasnrrrsafsikvvgvsdsrsyasgrnldissiisnkektgrisdr afsgpedlmgeaadllvdctpasrdgvreyslyrmafesgmnvvtanksglankwhdimdsanqnskyi ryeatvaggvplfsvldysilpskvkrfrgivsstinyvirnmangrslrdvvddaikkgiaesnpqdd lngldaarksvilvnhifgteytlndveysgvdersynandrlvtevyvddrrpvavsriislnkddfl msigmdglgyqietdsngtvnvsdiydgpyetagavvndilllskvqk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.95 Rfree 0.193
    Matthews' coefficent 2.69 Rfactor 0.152
    Waters 215 Solvent Content 54.24

    Ligand Information



    Protein Summary

    Pfam Annotation: This protein now has two pfam domains on it: NAD_binding_3 (PF03447)and Homoserine_dh (PF00742), both of which have many structures



    Gene NP_394635.1 from Thermoplasma Acidophilum encodes a protein with 324 residues consisting of two domains, N-terminal domian (2-118) and C-terminal Domain(119-324).  This target has been annotated homoserine dehydrogenase related protein   initially.  FFAS and SSM suggest this target is a structural homolog mainly to homoserine dehydrogenase (PDB ID: 1Q7G, 1EBF) with conserved residues in the active site. One NAD(P)H from bacteria natural processing is found and modeled in the conserved active site, consisting of K117, glu201, Asp 207 and Asp 212.  One Ca2+ is also modeled in the structure.   The interface interaction indicates that the biomolecule of protein NP_394635.1  should be a dimer.



    Figure 1. Protein NP_394635.1  monomer has a conserved active site in N-terminal near

    the interface between N-terminal and C-terminal. One NAD(P)H is modeled in the structure.




    Figure 2.  The biomolecule of NP_394635.1 is a dimer.






    Figure 3.  Protein NP_394635.1 (green) is a structural homolog to 1Q7G(Blue), 1EBF(Magenta)

    and JCSG target 3DO5(Yellow).






    Figure 4. The binding of NAD(P)H in the conserved active sited indicates a big movement of the loop(green, residue 195~206), which is not seen its structural homologus.








    1.     DeLaBarre, B.,  Thompson, P.R.,  Wright, G.D.,  Berghuis, A.M.   (2000) Crystal structures of homoserine dehydrogenase suggest a novel catalytic mechanism for oxidoreductases.  Nat.Struct.Biol.   7: 238-244   
    2.    Jacques, S.L.,  Mirza, I.A.,  Ejim, L.,  Koteva, K.,  Hughes, D.W.,  Green, K.,  Kinach, R.,  Honek, J.F.,  Lai, H.K.,  Berghuis, A.M.,  Wright, G.D.  (2003) Enzyme assisted suicide: Molecular basis for the antifungal activity of 5-hydroxy-4-oxonorvaline by potent inhibition of homoserine dehydrogenase  Chem.Biol.   10: 989-995   






















    Ligand Summary




    No references found.

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