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The Open Protein Structure Annotation Network
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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.
Site JCSG
PDB Id 3ing Target Id 380082
Molecular Characteristics
Source Thermoplasma acidophilum
Alias Ids NP_394635.1 Molecular Weight 35603.14 Da.
Residues 324 Isoelectric Point 5.44
Sequence mkeiriilmgtgnvglnvlriidasnrrrsafsikvvgvsdsrsyasgrnldissiisnkektgrisdra fsgpedlmgeaadllvdctpasrdgvreyslyrmafesgmnvvtanksglankwhdimdsanqnskyir yeatvaggvplfsvldysilpskvkrfrgivsstinyvirnmangrslrdvvddaikkgiaesnpqddl ngldaarksvilvnhifgteytlndveysgvdersynandrlvtevyvddrrpvavsriislnkddflm sigmdglgyqietdsngtvnvsdiydgpyetagavvndilllskvqk
  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
Ligands NDP (NADPH) x 1;EDO (1,2-ETHANEDIOL) x 6
Metals NA (SODIUM) x 1
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Protein Summary

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.

 

380082_1.png

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.

 

 

380082_2.png

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

 

 

380082_3.png

 


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

and JCSG target 3DO5(Yellow).


 

 

380082_5.png

 

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.

 


 


 

References,

 

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

Reviews

References

 

No references found.

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