PDBsum entry 2p9c

Oxidoreductase

PDB id: 2p9c

Contents

Protein chains

405 a.a. *

Ligands

NAI ×2

SER ×2

Waters ×54

* Residue conservation analysis

PDB id:

2p9c

Name:

Oxidoreductase

Title:

Crystal structure of serine bound g336v mutant of e.Coli phosphoglycerate dehydrogenase

Structure:

D-3-phosphoglycerate dehydrogenase. Chain: a, b. Synonym: pgdh. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: sera. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.46Å R-factor: 0.222 R-free: 0.281

Authors:

S.Dey,J.C.Sacchettini

Key ref:

S.Dey et al. (2007). The effect of hinge mutations on effector binding and domain rotation in e. coli D-3-phosphoglycerate dehydrogenase. J Biol Chem, 282, 18418-18426. PubMed id: 17459882 DOI: 10.1074/jbc.M701174200

Date:

24-Mar-07 Release date: 24-Apr-07

Protein chains

P0A9T0  (SERA_ECOLI) -  D-3-phosphoglycerate dehydrogenase from Escherichia coli (strain K12)

Seq: 410 a.a.

Struc: 405 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.1.1.1.399 - 2-oxoglutarate reductase.
• Reaction: (R)-2-hydroxyglutarate + NAD⁺ = 2-oxoglutarate + NADH + H⁺

(R)-2-hydroxyglutarate (Bound ligand (Het Group name = SER) matches with 41.67% similarity) + NAD(+) (Bound ligand (Het Group name = NAI) corresponds exactly) = 2-oxoglutarate + NADH + H(+)

• Enzyme class 2: E.C.1.1.1.95 - phosphoglycerate dehydrogenase.
• Reaction: (2R)-3-phosphoglycerate + NAD⁺ = 3-phosphooxypyruvate + NADH + H⁺

(2R)-3-phosphoglycerate + NAD(+) (Bound ligand (Het Group name = NAI) corresponds exactly) = 3-phosphooxypyruvate + NADH + H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1074/jbc.M701174200

J Biol Chem 282:18418-18426 (2007)

PubMed id: 17459882

The effect of hinge mutations on effector binding and domain rotation in e. coli D-3-phosphoglycerate dehydrogenase.

S.Dey, Z.Hu, X.L.Xu, J.C.Sacchettini, G.A.Grant.

ABSTRACT

D-3-Phosphoglycerate dehydrogenase (PGDH1, EC 1.1.1.95) from Escherichia coli contains two Gly-Gly sequences that have previously been shown to have the characteristics of hinge regions. One of these, G336-G337, is found in the loop between the substrate binding domain and the regulatory domain. Changing these glycine residues to valine affects the sensitivity of the enzyme to inhibition by L-serine, but not the extent of inhibition. The decrease in sensitivity is caused primarily by a decrease in the enzymes affinity for L-serine. These mutations also affect the domain rotation of the subunits in response to L-serine binding. A major conclusion of this study is that it defines a minimal limit on the necessary conformational changes leading to inhibition of enzyme activity. That is, some of the conformational differences seen in the native enzyme upon L-serine binding are not critical for inhibition, while others are maintained and may play important roles in inhibition and cooperativity. The structure of G336V, demonstrates that the minimal effect of L-serine binding leading to inhibition of enzyme activity requires a domain rotation of approximately only six degrees in just two of the four subunits of the enzyme that are oriented diagonally across from each other in the tetramer. Moreover, the structures show that both pairs of Asn-190 to Asn-190 hydrogen bonds across the subunit interfaces are necessary for activity. These observations are consistent with the half-the-sites activity, flip-flop mechanism, proposed for this and other similar enzymes, and suggest that the Asn-190 hydrogen bonds may function in the conformational transition between alternate half-the-site active forms of the enzyme.

Selected figure(s)

Figure 2.
FIGURE 2. Comparison of G336V PGDH with native PGDH. Left, comparison of L-serine binding to native PGDH ( ) and G336V PGDH ( ). The data are plotted as in Fig. 1. Right, comparison of the inhibition of enzymatic activity by L-serine in native PGDH ( ) and G336V PGDH ( ). The fractional inhibition of enzymatic activity (Inhibition) is plotted versus the total concentration of L-serine.

Figure 4.
FIGURE 4. Superposition of G336V,G337V + serine with G336V tetramers. Left, the figure depicts a superposition of serine-bound G336V,G337V double mutant onto a G336V tetramer. The serine-bound G336V,G337V tetramer is generated using the symmetry-related molecules. Subunit A and C are colored orange, and subunits B and D are colored pink. In the G336V structure, the subunits A and C are colored with shades of green, and subunits B and D are colored with shades of blue. Subunits A and C of G336V,G337V + serine superimpose well on the respective A and C subunits of the G336V serine-free enzyme. In subunits B and D, there is rotation of the nucleotide binding domain of 10-12°. In both the tetramers, ligands are not shown for the purpose of clarity. Right, detailed view of the hydrogen bond interaction at Asn^190 of subunits A and C of G336V,G337V + serine. In subunits B and D (pink), the Asn^190 residues are separated by too great a distance to form hydrogen bond contacts.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 18418-18426) copyright 2007.

Figures were selected by the author.