PDBsum entry: 1hfk

Hydrolase

PDB id: 1hfk

Contents

Protein chains

310 a.a. *

Ligands

SO4 ×2

Waters ×423

* Residue conservation analysis

PDB id:

1hfk

Name:

Hydrolase

Title:

Asparaginase from erwinia chrysanthemi, hexagonal form with weak sulfate

Structure:

L-asparagine amidohydrolase. Chain: a, c. Synonym: l-asparaginase, 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.

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.17Å R-factor: 0.199 R-free: 0.252

Authors:

J.Lubkowski,G.J.Palm,M.Kozak,M.Jaskolski,A.Wlodawer

Key ref:

M.Jaskólski et al. (2001). Structures of two highly homologous bacterial L-asparaginases: a case of enantiomorphic space groups. Acta Crystallogr D Biol Crystallogr, 57, 369-377. PubMed id: 11223513 DOI: 10.1107/S0907444900020175

Date:

05-Dec-00 Release date: 07-Dec-00

Protein chains

P06608  (ASPG_ERWCH) -  L-asparaginase

Seq: 348 a.a.

Struc: 310 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.5.1.1 - Asparaginase.
• Reaction: L-asparagine + H₂O = L-aspartate + NH₃

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

 Gene Ontology (GO) functional annotation 

• Biological process: cellular amino acid metabolic process (2 terms)
• Biochemical function: hydrolase activity (2 terms)

Added reference

DOI no: 10.1107/S0907444900020175

Acta Crystallogr D Biol Crystallogr 57:369-377 (2001)

PubMed id: 11223513

Structures of two highly homologous bacterial L-asparaginases: a case of enantiomorphic space groups.

M.Jaskólski, M.Kozak, J.Lubkowski, G.Palm, A.Wlodawer.

ABSTRACT

Quasi-enantiomorphic crystals of the Y25F mutant of Escherichia coli L-asparaginase and of the native Erwinia chrysanthemi L-asparaginase were obtained in the hexagonal space groups P6(5)22 and P6(1)22, respectively. The structures of these highly homologous enzymes were solved by molecular replacement and were refined with data extending to 2.2-2.5 A. These structures were compared with each other, as well as with other L-asparaginase structures previously observed with different crystal packing. It is concluded that the observed phenomenon, which is rare, was most likely to have arisen by chance.

Selected figure(s)

Figure 3.
Figure 3 Stereoviews of the arrangement of the tetramers of EcA(Y25F) (upper panel) and ErA (lower panel) along the sixfold screw axes. The orientation of both lattices is the same. Only the C^ atoms (represented by the spheres) are shown, uniquely colored as in Fig. 1-. The intimate dimers are formed by monomers A and C (green and blue) or B and D (red and yellow). The asymmetric unit of ErA consists of one intimate dimer. In the case of EcA, the asymmetric unit is formed by a looser dimer and the intimate dimers are formed across a crystallographic twofold axis.

Figure 5.
Figure 5 Crystal contacts mapped on the solvent-accessible surfaces of the EcA (left) and ErA (right) tetramers. In both tetramers, shown in identical orientation, only dimers are crystallographically unique. A list of crystal contacts that are shorter than 6.6 Å was generated using the program WHAT IF (Vriend, 1990[Vriend, G. (1990). J. Mol. Graph. 8, 52-56.]). All intratetramer contacts were disregarded. Residues participating in crystal packing interactions are labeled.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 369-377) copyright 2001.

Figures were selected by the author.