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Amino acid dehydrogenase PDB id
1bxg
Jmol
Contents
Protein chains
349 a.a. *
Ligands
NAD ×2
HCI ×2
PO4
Metals
__K
Waters ×175
* Residue conservation analysis
PDB id:
1bxg
Name: Amino acid dehydrogenase
Title: Phenylalanine dehydrogenase structure in ternary complex with NAD+ and beta-phenylpropionate
Structure: Phenylalanine dehydrogenase. Chain: a. Engineered: yes. Phenylalanine dehydrogenase. Chain: b. Engineered: yes
Source: Rhodococcus sp.. Organism_taxid: 1831. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.170    
Authors: J.L.Vanhooke,J.B.Thoden,N.M.W.Brunhuber,J.L.Blanchard, H.M.Holden
Key ref:
J.L.Vanhooke et al. (1999). Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism. Biochemistry, 38, 2326-2339. PubMed id: 10029526 DOI: 10.1021/bi982244q
Date:
02-Oct-98     Release date:   18-May-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q59771  (Q59771_RHOSO) -  L-phenylalanine dehydrogenase
Seq:
Struc: 		356 a.a.
349 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.4.1.20  - Phenylalanine dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-phenylalanine + H2O + NAD+ = phenylpyruvate + NH3 + NADH
L-phenylalanine
Bound ligand (Het Group name = HCI)
matches with 91.00% similarity 		+ H(2)O
 +
NAD(+)
Bound ligand (Het Group name = NAD)
corresponds exactly 		= phenylpyruvate
 + NH(3)
 + NADH
      Cofactor: Calcium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi982244q Biochemistry 38:2326-2339 (1999)
PubMed id: 10029526  
 
 
Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism.
J.L.Vanhooke, J.B.Thoden, N.M.Brunhuber, J.S.Blanchard, H.M.Holden.
 
  ABSTRACT  
 
The molecular structures of recombinant L-phenylalanine dehydrogenase from Rhodococcus sp. M4 in two different inhibitory ternary complexes have been determined by X-ray crystallographic analyses to high resolution. Both structures show that L-phenylalanine dehydrogenase is a homodimeric enzyme with each monomer composed of distinct globular N- and C-terminal domains separated by a deep cleft containing the active site. The N-terminal domain binds the amino acid substrate and contributes to the interactions at the subunit:subunit interface. The C-terminal domain contains a typical Rossmann fold and orients the dinucleotide. The dimer has overall dimensions of approximately 82 A x 75 A x 75 A, with roughly 50 A separating the two active sites. The structures described here, namely the enzyme.NAD+.phenylpyruvate, and enzyme. NAD+.beta-phenylpropionate species, represent the first models for any amino acid dehydrogenase in a ternary complex. By analysis of the active-site interactions in these models, along with the currently available kinetic data, a detailed chemical mechanism has been proposed. This mechanism differs from those proposed to date in that it accounts for the inability of the amino acid dehydrogenases, in general, to function as hydroxy acid dehydrogenases.
 

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
18491387 S.M.Tripathi, and R.Ramachandran (2008).
Crystal structures of the Mycobacterium tuberculosis secretory antigen alanine dehydrogenase (Rv2780) in apo and ternary complex forms captures "open" and "closed" enzyme conformations.
  Proteins, 72, 1089-1095.
PDB codes: 2voe 2voj
  18453703 S.M.Tripathi, and R.Ramachandran (2008).
Overexpression, purification, crystallization and preliminary X-ray analysis of Rv2780 from Mycobacterium tuberculosis H37Rv.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 367-370.  
14622249 S.Y.Seah, K.L.Britton, D.W.Rice, Y.Asano, and P.C.Engel (2003).
Kinetic analysis of phenylalanine dehydrogenase mutants designed for aliphatic amino acid dehydrogenase activity with guidance from homology-based modelling.
  Eur J Biochem, 270, 4628-4634.  
12192068 C.A.Bottoms, P.E.Smith, and J.J.Tanner (2002).
A structurally conserved water molecule in Rossmann dinucleotide-binding domains.
  Protein Sci, 11, 2125-2137.  
12037317 T.A.Muranova, S.N.Ruzheinikov, S.E.Sedelnikova, P.J.Baker, A.Pasquo, A.Galkin, N.Esaki, T.Ohshima, K.Soda, and D.W.Rice (2002).
Crystallization and preliminary X-ray analysis of substrate complexes of leucine dehydrogenase from Thermoactinomyces intermedius.
  Acta Crystallogr D Biol Crystallogr, 58, 1059-1062.  
11418766 B.Guillot, C.Lecomte, A.Cousson, C.Scherf, and C.Jelsch (2001).
High-resolution neutron structure of nicotinamide adenine dinucleotide.
  Acta Crystallogr D Biol Crystallogr, 57, 981-989.  
11722565 X.G.Wang, K.L.Britton, T.J.Stillman, D.W.Rice, and P.C.Engel (2001).
Conversion of a glutamate dehydrogenase into methionine/norleucine dehydrogenase by site-directed mutagenesis.
  Eur J Biochem, 268, 5791-5799.  
  11106178 M.Cirilli, G.Scapin, A.Sutherland, J.C.Vederas, and J.S.Blanchard (2000).
The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate.
  Protein Sci, 9, 2034-2037.
PDB code: 1f06
10924111 N.M.Brunhuber, J.B.Thoden, J.S.Blanchard, and J.L.Vanhooke (2000).
Rhodococcus L-phenylalanine dehydrogenase: kinetics, mechanism, and structural basis for catalytic specificity.
  Biochemistry, 39, 9174-9187.
PDB codes: 1c1d 1c1x
11123955 R.Zheng, and J.S.Blanchard (2000).
Identification of active site residues in E. coli ketopantoate reductase by mutagenesis and chemical rescue.
  Biochemistry, 39, 16244-16251.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.