PDBsum entry 1zlp

Lyase

PDB id: 1zlp

Contents

Protein chains

284 a.a. *

Ligands

GAQ ×2

Metals

_MG ×2

Waters ×69

* Residue conservation analysis

PDB id:

1zlp

Name:

Lyase

Title:

Petal death protein psr132 with cysteine-linked glutaraldehyde forming a thiohemiacetal adduct

Structure:

Petal death protein. Chain: a, b. Synonym: psr132. Engineered: yes

Source:

Dianthus caryophyllus. Clove pink. Organism_taxid: 3570. Gene: psr132. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.70Å R-factor: 0.200 R-free: 0.250

Authors:

A.Teplyakov,S.Liu,Z.Lu,A.Howard,D.Dunaway-Mariano,O.Herzberg

Key ref:

A.Teplyakov et al. (2005). Crystal structure of the petal death protein from carnation flower. Biochemistry, 44, 16377-16384. PubMed id: 16342930 DOI: 10.1021/bi051779y

Date:

08-May-05 Release date: 03-Jan-06

Protein chains

Q05957  (PDP_DIACA) -  Petal death protein from Dianthus caryophyllus

Seq: 318 a.a.

Struc: 284 a.a.

Enzyme reactions

• Enzyme class 1: E.C.3.7.1.1 - oxaloacetase.
• Reaction: oxaloacetate + H2O = oxalate + acetate + H⁺

oxaloacetate (Bound ligand (Het Group name = GAQ) matches with 45.45% similarity) + H2O = oxalate + acetate + H(+)

• Enzyme class 2: E.C.4.1.3.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1021/bi051779y

Biochemistry 44:16377-16384 (2005)

PubMed id: 16342930

Crystal structure of the petal death protein from carnation flower.

A.Teplyakov, S.Liu, Z.Lu, A.Howard, D.Dunaway-Mariano, O.Herzberg.

ABSTRACT

Expression of the PSR132 protein from Dianthus caryophyllus (carnation, clover pink) is induced in response to ethylene production associated with petal senescence, and thus the protein is named petal death protein (PDP). Recent work has established that despite the annotation of PDP in sequence databases as carboxyphosphoenolpyruvate mutase, the enzyme is actually a C-C bond cleaving lyase exhibiting a broad substrate profile. The crystal structure of PDP has been determined at 2.7 A resolution, revealing a dimer-of-dimers oligomeric association. Consistent with sequence homology, the overall alpha/beta barrel fold of PDP is the same as that of other isocitrate lyase/PEP mutase superfamily members, including a swapped eighth helix within a dimer. Moreover, Mg(2+) binds in the active site of PDP with a coordination pattern similar to that seen in other superfamily members. A compound, covalently bound to the catalytic residue, Cys144, was interpreted as a thiohemiacetal adduct resulting from the reaction of glutaraldehyde used to cross-link the crystals. The Cys144-carrying flexible loop that gates access to the active site is in the closed conformation. Models of bound substrates and comparison with the closed conformation of isocitrate lyase and 2-methylisocitrate lyase revealed the structural basis for the broad substrate profile of PDP.