PDBsum entry 2hoz

Isomerase

PDB id: 2hoz

Contents

Protein chains

427 a.a. *

Ligands

PMP ×2

HOZ

Waters ×597

* Residue conservation analysis

PDB id:

2hoz

Name:

Isomerase

Title:

Inter-subunit signaling in gsam

Structure:

Glutamate-1-semialdehyde 2,1-aminomutase (gsam) pmp-form. Chain: a, b. Synonym: gsa, glutamate-1-semialdehyde aminotransferase, gsa-at. Engineered: yes

Source:

Synechococcus elongatus. Organism_taxid: 269084. Strain: pcc 6301. Gene: heml, gsa. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.197 R-free: 0.250

Authors:

J.Stetefeld

Key ref:

J.Stetefeld et al. (2006). Intersubunit signaling in glutamate-1-semialdehyde-aminomutase. Proc Natl Acad Sci U S A, 103, 13688-13693. PubMed id: 16954186 DOI: 10.1073/pnas.0600306103

Date:

17-Jul-06 Release date: 22-Aug-06

Protein chains

P24630  (GSA_SYNP6) -  Glutamate-1-semialdehyde 2,1-aminomutase from Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)

Seq: 433 a.a.

Struc: 427 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.5.4.3.8 - glutamate-1-semialdehyde 2,1-aminomutase.
• Pathway: Porphyrin Biosynthesis (early stages)
• Reaction: (S)-4-amino-5-oxopentanoate = 5-aminolevulinate

(S)-4-amino-5-oxopentanoate (Bound ligand (Het Group name = HOZ) matches with 80.00% similarity) = 5-aminolevulinate

• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PMP) matches with 88.24% similarity)

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

reference

DOI no: 10.1073/pnas.0600306103

Proc Natl Acad Sci U S A 103:13688-13693 (2006)

PubMed id: 16954186

Intersubunit signaling in glutamate-1-semialdehyde-aminomutase.

J.Stetefeld, M.Jenny, P.Burkhard.

ABSTRACT

Enzymes are highly dynamic and tightly controlled systems. However, allosteric communication linked to catalytic turnover is poorly understood. We have performed an integrated approach to trap several catalytic intermediates in the alpha2-dimeric key enzyme of chlorophyll biosynthesis, glutamate-1-semialdehyde aminomutase. Our data reveal an active-site "gating loop," which undergoes a dramatic conformational change during catalysis, that is simultaneously open in one subunit and closed in the other. This loop movement requires a beta-sheet-to-alpha-helix transition to assume the closed conformation, thus facilitating transport of substrate toward, and concomitantly forming, an integral part of the active site. The accompanying intersubunit cross-talk, which controls negative cooperativity between the allosteric pair, was explored at the atomic level. The central elements of the communication triad are the cofactor bound to different catalytic intermediates, the interface helix, and the gating loop. Together, they form a molecular switch in which the cofactor acts as a central signal transmitter linking the subunit interface with the gating loop.

Selected figure(s)

Figure 1.
Crystal structure of GSAM in the PMP (KE-4)/PLP (DAVA-IA) form. (A) Overall stereo presentation of α2-dimeric GSAM. In subunit A, the N- and C-terminal domains as well as the cofactor binding domain are shown in different blue tones. Subunit B is shown in yellow. Cofactors and catalytic intermediates are highlighted. Both termini are denoted. The gating-loop regions disobeying local 2-fold symmetry and the interface helices (residues 121–138) are shown in blue (open) and red (closed), respectively. The gating loop is located at the dimer interface and extends toward the active site in the closed conformation. (B) Superposition of residues 150–183 in open (light blue/blue) and closed (yellow/red) conformation. Cofactors within the active sites are colored accordingly. The hinge element (Leu-158 and Ser-172) and Ser-163 are denoted. The β-hydroxy group of Ser-163 moves ≈22 Å.

Figure 2.
Transition of the gating loop between opened, closed, and reopened conformation. (A) View of the opened gating loop from the crystal structure of the double PMP form of GSAM (2). Fixation of DAVA with its 4′-amino group suggests that the gating loop offers a channeling mechanism to transport substrate into the active-site pocket. The backbone helix is suggested to be the anchoring point for GluTR (26). (B) Active-site pocket in the closed gating-loop conformation. Shown is a superposition of intermediate step iii/preparation 3 (stick-and-ball mode and water as red spheres) and step iv/preparation 4 (in yellow). In the external aldimine, the carboxy group fixation of the intermediate is mediated by three water molecules (W1–W3) and Ser-29. In the DAVA-IA state, all hydrogen bonds between the catalytic intermediate and the water molecules are disrupted and W3 is replaced by the carboxy group of DAVA. (C) Active-site pocket in the reopened and disordered gating-loop conformation. Shown is a superposition of step vi/preparation 4 (stick-and-ball mode and water as red spheres) and step iv/preparation 3 (in yellow). Electrostatic interactions of the catalytic intermediate with Tyr-301* and Ser-163 are absent. In KE-4 and EA-5, Glu-406 reveals multiple conformations and the carboxy group of ketimine-4 interacts again with waters W2 and W3. Dotted lines in black and yellow indicate hydrogen bonds in the EA-5/KE-4 and the DAVA-IA states, respectively. Residues marked with an asterisk depict the other subunit.

Figures were selected by an automated process.