PDBsum entry: 1dcn

Eye lens protein

PDB id: 1dcn

Contents

Protein chains

424 a.a. *

Ligands

AS1

Waters ×471

* Residue conservation analysis

PDB id:

1dcn

Name:

Eye lens protein

Title:

Inactive mutant h162n of delta 2 crystallin with bound argininosuccinate

Structure:

Delta 2 crystallin. Chain: a, b, c, d. Synonym: ddc2. Engineered: yes. Mutation: yes. Other_details: argininosuccinate bound to one active site

Source:

Anas platyrhynchos. Organism_taxid: 8839. Cell_line: 293. Organ: eye. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Homo-Tetramer (from PDB file)

Resolution:

2.30Å R-factor: 0.229 R-free: 0.290

Authors:

F.Vallee,M.A.Turner,P.Lindley,P.L.Howell

Key ref:

F.Vallée et al. (1999). Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate. Biochemistry, 38, 2425-2434. PubMed id: 10029536 DOI: 10.1021/bi982149h

Date:

29-Oct-98 Release date: 27-Apr-99

Protein chains

P24058  (ARLY2_ANAPL) -  Argininosuccinate lyase

Seq: 468 a.a.

Struc: 424 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.3.2.1 - Argininosuccinate lyase.
• Pathway: Urea Cycle and Arginine Biosynthesis
• Reaction: 2-(N(omega)-L-arginino)succinate = fumarate + L-arginine

2-(N(omega)-L-arginino)succinate (Bound ligand (Het Group name = AS1) corresponds exactly) = fumarate + L-arginine

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

 Gene Ontology (GO) functional annotation 

• Biological process: cellular amino acid biosynthetic process (3 terms)
• Biochemical function: catalytic activity (4 terms)

reference

DOI no: 10.1021/bi982149h

Biochemistry 38:2425-2434 (1999)

PubMed id: 10029536

Crystal structure of an inactive duck delta II crystallin mutant with bound argininosuccinate.

F.Vallée, M.A.Turner, P.L.Lindley, P.L.Howell.

ABSTRACT

Delta-crystallin, the major soluble protein component of avian and reptilian eye lenses, is highly homologous to the urea cycle enzyme, argininosuccinate lyase (ASL). In duck lenses, there are two highly homologous delta crystallins, delta I and delta II, that are 94% identical in amino acid sequence. While delta II crystallin has been shown to exhibit ASL activity in vitro, delta I is enzymatically inactive. The X-ray structure of a His to Asn mutant of duck delta II crystallin (H162N) with bound argininosuccinate has been determined to 2.3 A resolution using the molecular replacement technique. The overall fold of the protein is similar to other members of the superfamily to which this protein belongs, with the active site located in a cleft formed by three different monomers in the tetramer. The active site of the H162N mutant structure reveals that the side chain of Glu 296 has a different orientation relative to the homologous residue in the H91N mutant structure [Abu-Abed et al. (1997) Biochemistry 36, 14012-14022]. This shift results in the loss of the hydrogen bond between His 162 and Glu 296 seen in the H91N and turkey delta I crystallin structures; this H-bond is believed to be crucial for the catalytic mechanism of ASL/delta II crystallin. Argininosuccinate was found to be bound to residues in each of the three monomers that form the active site. The fumarate moiety is oriented toward active site residues His 162 and Glu 296 and other residues that are part of two of the three highly conserved regions of amino acid sequence in the superfamily, while the arginine moiety of the substrate is oriented toward residues which belong to either domain 1 or domain 2. The analysis of the structure reveals that significant conformational changes occur on substrate binding. The comparison of this structure with the inactive turkey delta I crystallin reveals that the conformation of domain 1 is crucial for substrate affinity and that the delta I protein is almost certainly inactive because it can no longer bind the substrate.