Protein Family Models

This domain is found in the D-3-phosphoglycerate dehydrogenase enzyme. In the structure of the Mycobacterium tuberculosis enzyme this domain was described as the intervening domain, also known as the allosteric substrate binding domain (ASB) [1,2,3]. The intervening domain between the substrate-binding and regulatory domains is not present in E. coli PGDH. This domain is closely related to Pfam:PF03315. It serves as an anion-binding site and may function as an allosteric site for the control of enzyme activity [3]. Paper describing PDB structure 1ygy. [1]. 15668249. Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits. Dey S, Grant GA, Sacchettini JC;. J Biol Chem. 2005;280:14892-14899. Paper describing PDB structure 3ddn. [2]. 18627175. Structural analysis of substrate and effector binding in Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase. Dey S, Burton RL, Grant GA, Sacchettini JC;. Biochemistry. 2008;47:8271-8282. [3]. 22023909. Contrasting catalytic and allosteric mechanisms for phosphoglycerate dehydrogenases. Grant GA;. Arch Biochem Biophys. 2012;519:175-185. (from Pfam)

Date:

2024-10-16

This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family Pfam:PF00389. [1]. 9126843. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. Dengler U, Niefind K, Kiess M, Schomburg D;. J Mol Biol 1997;267:640-660. (from Pfam)

Date:

2024-10-16

This family of domains generally have a regulatory role. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. The ACT domain is found in: D-3-phosphoglycerate dehydrogenase EC:1.1.1.95 Swiss:P08328, which is inhibited by serine [1]. Aspartokinase EC:2.7.2.4 Swiss:P53553, which is regulated by lysine. Acetolactate synthase small regulatory subunit Swiss:P00894, which is inhibited by valine. Phenylalanine-4-hydroxylase EC:1.14.16.1 Swiss:P00439, which is regulated by phenylalanine. Prephenate dehydrogenase EC:4.2.1.51 Swiss:P21203. formyltetrahydrofolate deformylase EC:3.5.1.10, Swiss:P37051, which is activated by methionine and inhibited by glycine. GTP pyrophosphokinase EC:2.7.6.5 Swiss:P11585 [1]. 7719856. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Schuller DJ, Grant GA, Banaszak LJ;. Nat Struct Biol 1995;2:69-76. Definition of the domain. [2]. 10222208. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. Aravind L, Koonin EV;. J Mol Biol 1999;287:1023-1040. (from Pfam)

Date:

2024-10-16

This family represents the largest portion of the catalytic domain of 2-hydroxyacid dehydrogenases as the NAD binding domain is inserted within the structural domain. [1]. 9126843. Crystal structure of a ternary complex of D-2-hydroxyisocaproate dehydrogenase from Lactobacillus casei, NAD+ and 2-oxoisocaproate at 1.9 A resolution. Dengler U, Niefind K, Kiess M, Schomburg D;. J Mol Biol 1997;267:640-660. (from Pfam)

Date:

2024-10-16

This HMM represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli.

Gene:

serA

Date:

2021-04-27

phosphoglycerate dehydrogenase catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, the first step in serine biosynthesis

Date:

2017-03-21