PDBsum entry 3fdd

Lyase

PDB id: 3fdd

Contents

Protein chain

502 a.a. *

Ligands

PLP

ACT

Metals

_CL

Waters ×212

* Residue conservation analysis

PDB id:

3fdd

Name:

Lyase

Title:

The crystal structure of the pseudomonas dacunhae aspartate-beta- decarboxylase reveals a novel oligomeric assembly for a pyridoxal-5- phosphate dependent enzyme

Structure:

L-aspartate-beta-decarboxylase. Chain: a. Engineered: yes

Source:

Pseudomonas dacunhae atcc 21192. Organism_taxid: 207291. Gene: aspd, gi:28875527. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.35Å R-factor: 0.170 R-free: 0.212

Authors:

S.Lima,B.Sundararaju,C.Huang,R.Khristoforov,C.Momany,R.S.Phillips

Key ref:

S.Lima et al. (2009). The crystal structure of the Pseudomonas dacunhae aspartate-beta-decarboxylase dodecamer reveals an unknown oligomeric assembly for a pyridoxal-5'-phosphate-dependent enzyme. J Mol Biol, 388, 98. PubMed id: 19265705 DOI: 10.1016/j.jmb.2009.02.055

Date:

25-Nov-08 Release date: 17-Mar-09

Protein chain

Q845W8  (Q845W8_COMTE) -  Aminotransferase from [Pseudomonas] dacunhae ATCC 21192

Seq: 533 a.a.

Struc: 502 a.a.

Enzyme reactions

• Enzyme class: E.C.2.6.1.- - ?????

DOI no: 10.1016/j.jmb.2009.02.055

J Mol Biol 388:98 (2009)

PubMed id: 19265705

The crystal structure of the Pseudomonas dacunhae aspartate-beta-decarboxylase dodecamer reveals an unknown oligomeric assembly for a pyridoxal-5'-phosphate-dependent enzyme.

S.Lima, B.Sundararaju, C.Huang, R.Khristoforov, C.Momany, R.S.Phillips.

ABSTRACT

The Pseudomonas dacunhael-aspartate-beta-decarboxylase (ABDC, aspartate 4-decarboxylase, aspartate 4-carboxylyase, E.C. 4.1.1.12) is a pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the beta-decarboxylation of l-aspartate to produce l-alanine and CO(2). This catalytically versatile enzyme is known to form functional dodecamers at its optimal pH and is thought to work in conjunction with an l-Asp/l-Ala antiporter to establish a proton gradient across the membrane that can be used for ATP biosynthesis. We have solved the atomic structure of ABDC to 2.35 A resolution using single-wavelength anomalous dispersion phasing. The structure reveals that ABDC oligomerizes as a homododecamer in an unknown mode among PLP-dependent enzymes and has highest structural homology with members of the PLP-dependent aspartate aminotransferase subfamily. The structure shows that the ABDC active site is very similar to that of aspartate aminotransferase. However, an additional arginine side chain (Arg37) was observed flanking the re-side of the PLP ring in the ABDC active site. The mutagenesis results show that although Arg37 is not required for activity, it appears to be involved in the ABDC catalytic cycle.

Selected figure(s)

Figure 3.
Fig. 3. (a) Ribbon representation of the ABDC dodecamer with each monomer labeled. Dimers forming the dodecamer are A–B, C–D, E–F, G–H, I–J, and K–L. Monomers I and J are at the back of the molecule and cannot be seen. (b) Surface renderings of the ABDC dimer (upper panel) formed between monomers A–B and C–D, with residues involved in oligomerization contacts (not dimer contacts) colored red. The bottom panel illustrates the spatial relationships between adjacent dimers A–B and C–D. Monomer D is transparent for clarity. Residues involved in forming the trimeric interface between monomers A–B–C are specified in the text.

Figure 5.
Fig. 5. Active sites of structurally superposed ABDC and ligand-bound E. coli AAT (PDB accession no. 1X2A). Note how Arg37 side-chain atoms closely align with the d-glutamate external aldimine carboxylate atoms. ABDC residues (labeled with asterisk ) are colored with white carbons, blue nitrogens, orange phosphorous, and red oxygens. Corresponding AAT residues are colored with green carbons. The following ABDC/AAT residues were omitted for clarity: Asp286/Asp222, Val288/Ala244, Ser311/Ser253, and Lys315/Lys258. Note the large conformational differences between the side chains of ABDC residues Arg372 and Arg497 and the corresponding residues of AAT, Arg292 and Arg386.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 388, 98) copyright 2009.

Figures were selected by an automated process.