PDBsum entry: 1hfw

Asparaginase

PDB-id: 1hfw

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

307 a.a. *

Ligands

GLU ×4

Waters ×961

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1hfw

Name:

Asparaginase

Title:

X-ray structure of the complex between erwinia chrysanthemi l-asparaginase and l-glutamate

Structure:

L-asparaginase. Chain: a, b, c, d. Synonym: l-asparagine amidohydrolase, l-asnase. Ec: 3.5.1.1

Source:

Erwinia chrysanthemi. Organism_taxid: 556. Strain: ncppb 1125. Other_details: the new name of erwinia chrysanthemi is pectobacterium chrysanthemi

Biological unit:

Tetramer (from PQS)

UniProt:

Chains A, B, C, D: P06608 (ASPG_ERWCH)

Seq:

Struc:

Seq:

348 a.a.

Struc:

307 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

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

Enzyme class:

E.C.3.5.1.1   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

L-asparagine + H₂O = L-aspartate + NH₃ (see diagram below)

Resolution:

1.8Å

R-factor:

0.168

R-free:

0.188

Authors:

J.Lubkowski,A.Wlodawer,K.A.Kolyani

Key ref:

K.Aghaiypour et al. (2001). Structural basis for the activity and substrate specificity of Erwinia chrysanthemi L-asparaginase.. Biochemistry, 40, 5655-5664. [PubMed id: 11341830] [DOI: 10.1021/bi0029595]

Date:

08-Dec-00

Release date:

07-Aug-01

Related entries:

1hfj asparaginase from erwinia chrysanthemi, hexagonal form with sulfate
1hfk asparaginase from erwinia chrysanthemi, hexagonal form with partial sulfate
1hg0 x-ray structure of the complex between erwinia chrysanthemi l-asparaginase and succinic acid
1hg1 x-ray structure of the complex between erwinia chrysanthemi l-asparaginase and d-aspartate

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1021/bi0029595

Biochemistry 40:5655-5664 (2001)

PubMed id: 11341830

Structural basis for the activity and substrate specificity of Erwinia chrysanthemi L-asparaginase.

K.Aghaiypour, A.Wlodawer, J.Lubkowski.

ABSTRACT

Bacterial L-asparaginases, enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid, have been used for over 30 years as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia. Other substrates of asparaginases include L-glutamine, D-asparagine, and succinic acid monoamide. In this report, we present high-resolution crystal structures of the complexes of Erwinia chrysanthemi L-asparaginase (ErA) with the products of such reactions that also can serve as substrates, namely L-glutamic acid (L-Glu), D-aspartic acid (D-Asp), and succinic acid (Suc). Comparison of the four independent active sites within each complex indicates unique and specific binding of the ligand molecules; the mode of binding is also similar between complexes. The lack of the alpha-NH3(+) group in Suc, compared to L-Asp, does not affect the binding mode. The side chain of L-Glu, larger than that of L-Asp, causes several structural distortions in the ErA active side. The active site flexible loop (residues 15-33) does not exhibit stable conformation, resulting in suboptimal orientation of the nucleophile, Thr15. Additionally, the delta-COO(-) plane of L-Glu is approximately perpendicular to the plane of gamma-COO(-) in L-Asp bound to the asparaginase active site. Binding of D-Asp to the ErA active site is very distinctive compared to the other ligands, suggesting that the low activity of ErA against D-Asp could be mainly attributed to the low k(cat) value. A comparison of the amino acid sequence and the crystal structure of ErA with those of other bacterial L-asparaginases shows that the presence of two active-site residues, Glu63(ErA) and Ser254(ErA), may correlate with significant glutaminase activity, while their substitution by Gln and Asn, respectively, may lead to minimal L-glutaminase activity.