PDBsum entry: 1bw9

Amino acid dehydrogenase

PDB-id

1bw9


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Description

Header details

Protein chains

Ligands

NAD ×2

PPY ×2

PO4

EDO ×3

IPA ×4

Metal ions

__K ×2

_NA ×2

Waters ×1021

* Residue conservation analysis

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PDB id:

1bw9

Name:

Amino acid dehydrogenase

Title:

Phenylalanine dehydrogenase structure in ternary complex with NAD+ and phenylpyruvate

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.

UniProt:

Chains A, B: Q59771 (Q59771_RHOSO)

Seq:

Struc:

Seq:

356 a.a.

Struc:

350 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme class:

E.C.1.4.1.20 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

L-phenylalanine + H₂O + NAD⁺ = phenylpyruvate + NH₃ + NADH (see diagram below)

Cofactor:

Calcium

Resolution:

1.50Å

R-factor:

0.195

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:

01-Oct-98

Release date:

18-May-99

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Enzyme reaction for E.C.1.4.1.20

L-phenylalanine

H(2)O

NAD(+)

phenylpyruvate
Bound ligand (Het Group name = 1PY)
corresponds exactly

NH(3)

NADH
Bound ligand (Het Group name = NAD)
corresponds exactly

Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Key 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

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

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.