Protein Family Models

This entry represents the ACT domain found at the N-terminal of acetohydroxyacid synthase isozyme III from Escherichia coli and similar sequences. Paper describing PDB structure 1psd. [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. Paper describing PDB structure 1sc6. [2]. 15035616. Multiconformational states in phosphoglycerate dehydrogenase. Bell JK, Grant GA, Banaszak LJ;. Biochemistry. 2004;43:3450-3458. Paper describing PDB structure 1yba. [3]. 15823035. Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase. Thompson JR, Bell JK, Bratt J, Grant GA, Banaszak LJ;. Biochemistry. 2005;44:5763-5773. Paper describing PDB structure 2f1f. [4]. 16458324. Structure of the regulatory subunit of acetohydroxyacid synthase isozyme III from Escherichia coli. Kaplun A, Vyazmensky M, Zherdev Y, Belenky I, Slutzker A, Mendel S, Barak Z, Chipman DM, Shaanan B;. J Mol Biol. 2006;357:951-963. Paper describing PDB structure 2fgc. [5]. 17586771. Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit. Petkowski JJ, Chruszcz M, Zimmerman MD, Zheng H, Skarina T, Onopriyenko O, Cymborowski MT, Koclega KD, Savchenko A, Edwards A, Minor W;. Protein Sci. 2007;16:1360-1367. (from Pfam)

Date:

2024-10-16

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