PDBsum entry 1s3n

Phosphodiesterase

PDB id: 1s3n

Contents

Protein chains

165 a.a. *

Metals

_MN ×4

Waters ×60

* Residue conservation analysis

PDB id:

1s3n

Name:

Phosphodiesterase

Title:

Structural and functional characterization of a novel archaeal phosphodiesterase

Structure:

Hypothetical protein mj0936. Chain: a, b. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.220 R-free: 0.253

Authors:

S.Chen,D.Busso,A.F.Yakunin,E.Kuznetsova,M.Proudfoot,J.Jancrick,R.Kim, S.-H.Kim,Berkeley Structural Genomics Center (Bsgc)

Key ref:

S.Chen et al. (2004). Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii. J Biol Chem, 279, 31854-31862. PubMed id: 15128743 DOI: 10.1074/jbc.M401059200

Date:

13-Jan-04 Release date: 10-Aug-04

Protein chains

Q58346  (P936_METJA) -  Phosphodiesterase MJ0936 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)

Seq: 166 a.a.

Struc: 165 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.4.- - ?????

DOI no: 10.1074/jbc.M401059200

J Biol Chem 279:31854-31862 (2004)

PubMed id: 15128743

Structural and functional characterization of a novel phosphodiesterase from Methanococcus jannaschii.

S.Chen, A.F.Yakunin, E.Kuznetsova, D.Busso, R.Pufan, M.Proudfoot, R.Kim, S.H.Kim.

ABSTRACT

Methanococcus jannaschii MJ0936 is a hypothetical protein of unknown function with over 50 homologs found in many bacteria and Archaea. To help define the molecular (biochemical and biophysical) function of MJ0936, we determined its crystal structure at 2.4-A resolution and performed a series of biochemical screens for catalytic activity. The overall fold of this single domain protein consists of a four-layered structure formed by two beta-sheets flanked by alpha-helices on both sides. The crystal structure suggested its biochemical function to be a nuclease, phosphatase, or nucleotidase, with a requirement for some metal ions. Crystallization in the presence of Ni(2+) or Mn(2+) produced a protein containing a binuclear metal center in the putative active site formed by a cluster of conserved residues. Analysis of MJ0936 against a panel of general enzymatic assays revealed catalytic activity toward bis-p-nitrophenyl phosphate, an indicator substrate for phosphodiesterases and nucleases. Significant activity was also found with two other phosphodiesterase substrates, thymidine 5'-monophosphate p-nitrophenyl ester and p-nitrophenylphosphorylcholine, but no activity was found for cAMP or cGMP. Phosphodiesterase activity of MJ0936 had an absolute requirement for divalent metal ions with Ni(2+) and Mn(2+) being most effective. Thus, our structural and enzymatic studies have identified the biochemical function of MJ0936 as that of a novel phosphodiesterase.

Selected figure(s)

Figure 4.
FIG. 4. A, ribbon representation of the MJ0936 monomer structure. Secondary structure elements are numbered accordingly. B, topology of the monomer structure. Helices are represented as green cylinders and strands are represented as yellow arrows. C, electrostatic potential surface of MJ0936 (red, negatively charged surface; blue, positively charged surface; white, uncharged surface).

Figure 5.
FIG. 5. A, superimposition of the overall structure in three crystal forms: native crystal (colored as blue), nickel complex (colored as red), and manganese complex (colored as green). The figure is shown in stereo diagram. Bound metals/ions are represented as a sphere model using the same color schemes as the corresponding protein backbones. B, superimposition of the active site residues in three crystal forms: native crystal (colored as blue), nickel complex (colored as red), and manganese complex (colored as green). The figure is shown in stereo diagram. Bound metals/ions are represented as a sphere model. Three residues in the native crystal form (His-120, Thr-121, and His-122) are individually labeled in blue. Three arrows in the figure indicate the conformation change of these three residues between native crystal structure and complex structures.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 31854-31862) copyright 2004.

Figures were selected by an automated process.