PDBsum entry 1et0

Lyase

PDB id: 1et0

Contents

Protein chain

254 a.a. *

Ligands

PLP

Waters ×126

* Residue conservation analysis

PDB id:

1et0

Name:

Lyase

Title:

Crystal structure of aminodeoxychorismate lyase from escherichia coli

Structure:

4-amino-4-deoxychorismate lyase. Chain: a. Synonym: adc lyase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.196 R-free: 0.279

Authors:

T.Nakai,H.Mizutani,I.Miyahara,K.Hirotsu,S.Takeda,K.H.Jhee, T.Yoshimura,N.Esaki

Key ref:

T.Nakai et al. (2000). Three-dimensional structure of 4-amino-4-deoxychorismate lyase from Escherichia coli. J Biochem (tokyo), 128, 29-38. PubMed id: 10876155

Date:

12-Apr-00 Release date: 19-Jul-00

Protein chain

P28305  (PABC_ECOLI) -  Aminodeoxychorismate lyase from Escherichia coli (strain K12)

Seq: 269 a.a.

Struc: 254 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.3.38 - aminodeoxychorismate lyase.
• Pathway: Folate Biosynthesis (late stages)
• Reaction: 4-amino-4-deoxychorismate = 4-aminobenzoate + pyruvate + H⁺
• Cofactor: Pyridoxal 5'-phosphate

Pyridoxal 5'-phosphate (Bound ligand (Het Group name = PLP) matches with 93.75% similarity)

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

reference

J Biochem (tokyo) 128:29-38 (2000)

PubMed id: 10876155

Three-dimensional structure of 4-amino-4-deoxychorismate lyase from Escherichia coli.

T.Nakai, H.Mizutani, I.Miyahara, K.Hirotsu, S.Takeda, K.H.Jhee, T.Yoshimura, N.Esaki.

ABSTRACT

4-Amino-4-deoxychorismate lyase (ADCL) is a member of the fold-type IV of PLP dependent enzymes that converts 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate and pyruvate. The crystal structure of ADCL from Escherichia coli has been solved using MIR phases in combination with density modification. The structure has been refined to an R-factor of 20.6% at 2.2 A resolution. The enzyme is a homo dimer with a crystallographic twofold axis, and the polypeptide chain is folded into small and large domains with an interdomain loop. The coenzyme, pyridoxal 5'-phosphate, resides at the domain interface, its re-face facing toward the protein. Although the main chain folding of the active site is homologous to those of D-amino acid and L-branched-chain amino acid aminotransferases, no residues in the active site are conserved among them except for Arg59, Lys159, and Glu193, which directly interact with the coenzyme and play critical roles in the catalytic functions. ADC was modeled into the active site of the unliganded enzyme on the basis of the X-ray structures of the unliganded and liganded forms in the D-amino acid and L-branched-chain amino acid aminotransferases. According to this model, the carboxylates of ADC are recognized by Asn256, Arg107, and Lys97, and the cyclohexadiene moiety makes van der Waals contact with the side chain of Leu258. ADC forms a Schiff base with PLP to release the catalytic residue Lys159, which forms a hydrogen bond with Thr38. The neutral amino group of Lys159 eliminates the a-proton of ADC to give a quinonoid intermediate to release a pyruvate in accord with the proton transfer from Thr38 to the olefin moiety of ADC.