PDBsum entry: 1fdz

Lyase

PDB id: 1fdz

Contents

Protein chains

292 a.a. *

Ligands

PYR ×4

Waters ×228

* Residue conservation analysis

PDB id:

1fdz

Name:

Lyase

Title:

N-acetylneuraminate lyase in complex with pyruvate via borohydride reduction

Structure:

N-acetylneuraminate lyase. Chain: a, b, c, d. Synonym: n-acetylneuraminic acid aldolase. Engineered: yes. Other_details: covalent complex, obtained by reduction with borohydride from an enzyme - sialic acid mix

Source:

Escherichia coli. Organism_taxid: 562. Strain: tg1. Gene: npl. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: described in lilley, g.G. Et al. (1992) see reference below. Obtained by borohydride reduction of enzyme in complex with sialic acid

Biol. unit:

Tetramer (from PQS)

Resolution:

2.60Å R-factor: 0.200

Authors:

M.C.Lawrence,J.A.R.G.Barbosa,B.J.Smith,N.E.Hall,P.A.Pilling, H.C.Ooi,S.M.Marcuccio

Key ref:

M.C.Lawrence et al. (1997). Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase. J Mol Biol, 266, 381-399. PubMed id: 9047371 DOI: 10.1006/jmbi.1996.0769

Date:

08-Jul-96 Release date: 22-Oct-97

Protein chains

P0A6L4  (NANA_ECOLI) -  N-acetylneuraminate lyase

Seq: 297 a.a.

Struc: 292 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.1.3.3 - N-acetylneuraminate lyase.
• Reaction: N-acetylneuraminate = N-acetyl-D-mannosamine + pyruvate

N-acetylneuraminate = N-acetyl-D-mannosamine + pyruvate (Bound ligand (Het Group name = PYR) matches with 83.00% similarity)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: metabolic process (3 terms)
• Biochemical function: catalytic activity (3 terms)

reference

DOI no: 10.1006/jmbi.1996.0769

J Mol Biol 266:381-399 (1997)

PubMed id: 9047371

Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase.

M.C.Lawrence, J.A.Barbosa, B.J.Smith, N.E.Hall, P.A.Pilling, H.C.Ooi, S.M.Marcuccio.

ABSTRACT

We describe here a sub-family of enzymes related both structurally and functionally to N-acetylneuraminate lyase. Two members of this family (N-acetylneuraminate lyase and dihydrodipicolinate synthase) have known three-dimensional structures and we now proceed to show their structural and functional relationship to two further proteins, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase and D-4-deoxy-5-oxoglucarate dehydratase. These enzymes are all thought to involve intermediate Schiff-base formation with their respective substrates. In order to understand the nature of this intermediate, we have determined the three-dimensional structure of N-acetylneuraminate lyase in complex with hydroxypyruvate (a product analogue) and in complex with one of its products (pyruvate). From these structures we deduce the presence of a closely similar Schiff-base forming motif in all members of the N-acetylneuraminate lyase sub-family. A fifth protein, MosA, is also confirmed to be a member of the sub-family although the involvement of an intermediate Schiff-base in its proposed reaction is unclear.

Selected figure(s)

Figure 2.
Figure 2. Diagram of the subunit tertiary structure of N- acetylneuraminate lyase. The b-strands of the (a/b)8 bar- rel are denoted a to h, while the helices are denoted A to H, with the three additional C-terminal helices being denoted I, J, and K, respectively (Izard et al., 1994). The side-chain of Lys165 protrudes into the active site cavity from strand f, and is shown here as complexed to hydroxypyruvate via N z . The Figure was generated using MOLSCRIPT (Kraulis, 1991).

Figure 5.
Figure 5. Conformational detail of the peptide loop formed by residues Ala44 to Glu50 in E. coli NAL and its inter- action with the hydroxypyruvate inhibitor. The peptide loop consists of two type I b-turns comprising residues 45 to 49 and 46 to 50, respectively. Glu50 forms a salt bridge with Lys256 (the latter residue is immediately outside the volume shown). Tyr110 and Tyr111 from a neighbouring monomer also interact with the loop via their O Z atoms. Residues of interest are highlighted in ball-and-stick representation, while surrounding residues are shown in copper- coloured stick-only representation. Hydrogen bonds are shown as yellow lines. The inhibitor (in a 2-deoxy-3-keto form, see the text) is complexed to Lys165 N z via a single bond to C(2), and its carboxylate moiety is positioned so as to make hydrogen bonds with Ser47 N and Thr48 O g1 and Tyr137 O Z . The inhibitor O(3) is capable of forming a hydrogen bond with Tyr137 O Z . A water molecule, coloured red and labelled H2O, is located beyond the inhibitor carboxylate in a pocket in the active site floor. Two other water molecules are also visible; these are located within the protein volume and are not accessible from within the active site cavity. The Figure was generated using MOL- SCRIPT (Kraulis, 1991).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 266, 381-399) copyright 1997.

Figures were selected by an automated process.