PDBsum entry 2a0f

Transferase/transferase regulator

PDB id: 2a0f

Contents

Protein chains

310 a.a. *

146 a.a. *

Ligands

PCT

Metals

_ZN ×2

Waters ×379

* Residue conservation analysis

PDB id:

2a0f

Name:

Transferase/transferase regulator

Title:

Structure of d236a mutant e. Coli aspartate transcarbamoylase in presence of phosphonoacetamide at 2.90 a resolution

Structure:

Aspartate carbamoyltransferase catalytic chain. Chain: a, c. Synonym: aspartate transcarbamylase, atcase. Engineered: yes. Mutation: yes. Aspartate carbamoyltransferase regulatory chain. Chain: b, d. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: pyrb. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: pyri.

Biol. unit:

Dodecamer (from PDB file)

Resolution:

2.90Å R-factor: 0.217 R-free: 0.279

Authors:

K.A.Stieglitz,K.J.Dusinberre,J.P.Cardia,H.Tsuruta,E.R.Kantrowitz

Key ref:

K.A.Stieglitz et al. (2005). Structure of the E.coli aspartate transcarbamoylase trapped in the middle of the catalytic cycle. J Mol Biol, 352, 478-486. PubMed id: 16120448 DOI: 10.1016/j.jmb.2005.07.046

Date:

16-Jun-05 Release date: 27-Sep-05

Protein chains

P0A786  (PYRB_ECOLI) -  Aspartate carbamoyltransferase catalytic subunit from Escherichia coli (strain K12)

Seq: 311 a.a.

Struc: 310 a.a.*

Protein chains

P0A7F3  (PYRI_ECOLI) -  Aspartate carbamoyltransferase regulatory chain from Escherichia coli (strain K12)

Seq: 153 a.a.

Struc: 146 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains A, C: E.C.2.1.3.2 - aspartate carbamoyltransferase.
• Pathway: Pyrimidine Biosynthesis
• Reaction: carbamoyl phosphate + L-aspartate = N-carbamoyl-L-aspartate + phosphate + H⁺

carbamoyl phosphate + L-aspartate = N-carbamoyl-L-aspartate + phosphate + H(+) (Bound ligand (Het Group name = PCT) matches with 44.44% similarity)

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

reference

DOI no: 10.1016/j.jmb.2005.07.046

J Mol Biol 352:478-486 (2005)

PubMed id: 16120448

Structure of the E.coli aspartate transcarbamoylase trapped in the middle of the catalytic cycle.

K.A.Stieglitz, K.J.Dusinberre, J.P.Cardia, H.Tsuruta, E.R.Kantrowitz.

ABSTRACT

Snapshots of the catalytic cycle of the allosteric enzyme aspartate transcarbamoylase have been obtained via X-ray crystallography. The enzyme in the high-activity high-affinity R state contains two catalytic chains in the asymmetric unit that are different. The active site in one chain is empty, while the active site in the other chain contains an analog of the first substrate to bind in the ordered mechanism of the reaction. Small angle X-ray scattering shows that once the enzyme is converted to the R state, by substrate binding, the enzyme remains in the R state until substrates are exhausted. Thus, this structure represents the active form of the enzyme trapped at two different stages in the catalytic cycle, before the substrates bind (or after the products are released), and after the first substrate binds. Opening and closing of the catalytic chain domains explains how the catalytic cycle occurs while the enzyme remains globally in the R-quaternary structure.

Selected figure(s)

Figure 3.
Figure 3. Stereoviews of the active site of the R236_PAM structure. (a) A simulated annealing 2F[o]−F[c] electron density map, contoured at 1.8σ, with PAM (magenta) omitted from the map calculation. Overlaid onto the electron density map are the refined positions of the residues. (b) Overlay of the active sites of the C1 (carbon atoms in light gray) and C6 (carbon atoms in dark gray) chains of the R[236_PAM] structure. The interactions between the enzyme and PAM in the C1 chain are shown as dotted lines. An asterisk after the residue number indicates that the residue is donated from the adjacent C2 chain. Figure 3. Stereoviews of the active site of the R236_PAM structure. (a) A simulated annealing 2F[o]−F[c] electron density map, contoured at 1.8σ, with PAM (magenta) omitted from the map calculation. Overlaid onto the electron density map are the refined positions of the residues. (b) Overlay of the active sites of the C1 (carbon atoms in light gray) and C6 (carbon atoms in dark gray) chains of the R[236_PAM] structure. The interactions between the enzyme and PAM in the C1 chain are shown as dotted lines. An asterisk after the residue number indicates that the residue is donated from the adjacent C2 chain.

Figure 4.
Figure 4. Complete active site of the C1 chain of the R[236_PAM] structure with PAM bound. The Asp shown is based on the position obtained using AUTODOCK.^14 The red arrow indicates the attack of the α-amino group of Asp onto the carbonyl carbon of PAM (distance 3.5 Å). Interactions to PAM and Asp are shown by black and red dotted lines respectively. Figure 4. Complete active site of the C1 chain of the R[236_PAM] structure with PAM bound. The Asp shown is based on the position obtained using AUTODOCK.[3]^14 The red arrow indicates the attack of the α-amino group of Asp onto the carbonyl carbon of PAM (distance 3.5 Å). Interactions to PAM and Asp are shown by black and red dotted lines respectively. This Figure was produced using POVScript+.[4]^33

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 478-486) copyright 2005.

Figures were selected by an automated process.