PDBsum entry 2g08

Hydrolase

PDB id: 2g08

Contents

Protein chains

291 a.a. *

Ligands

AF3 ×2

Metals

_MG ×2

Waters ×479

* Residue conservation analysis

PDB id:

2g08

Name:

Hydrolase

Title:

X-ray structure of mouse pyrimidine 5'-nucleotidase type 1, product- transition complex analog with aluminum fluoride

Structure:

Cytosolic 5'-nucleotidase iii. Chain: a, b. Synonym: cn-iii, pyrimidine 5'- nucleotidase 1, p5'n-1, p5n-1, pn-i, lupin. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: nt5c3. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.35Å R-factor: 0.194 R-free: 0.260

Authors:

E.Bitto,C.A.Bingman,G.E.Wesenberg,G.N.Phillips Jr.,Center For Eukaryotic Structural Genomics (Cesg)

Key ref:

E.Bitto et al. (2006). Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning. J Biol Chem, 281, 20521-20529. PubMed id: 16672222 DOI: 10.1074/jbc.M602000200

Date:

11-Feb-06 Release date: 04-Apr-06

Protein chains

Q9D020  (5NT3A_MOUSE) -  Cytosolic 5'-nucleotidase 3A from Mus musculus

Seq: 331 a.a.

Struc: 291 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.3.1.3.5 - 5'-nucleotidase.
• Reaction: a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate
• Enzyme class 2: E.C.3.1.3.91 - 7-methylguanosine nucleotidase.
• Reaction:
  1. N₇-methyl-GMP + H2O = N₇-methylguanosine + phosphate
  2. CMP + H2O = cytidine + phosphate

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: 10.1074/jbc.M602000200

J Biol Chem 281:20521-20529 (2006)

PubMed id: 16672222

Structure of pyrimidine 5'-nucleotidase type 1. Insight into mechanism of action and inhibition during lead poisoning.

E.Bitto, C.A.Bingman, G.E.Wesenberg, J.G.McCoy, G.N.Phillips.

ABSTRACT

Eukaryotic pyrimidine 5'-nucleotidase type 1 (P5N-1) catalyzes dephosphorylation of pyrimidine 5'-mononucleotides. Deficiency of P5N-1 activity in red blood cells results in nonspherocytic hemolytic anemia. The enzyme deficiency is either familial or can be acquired through lead poisoning. We present the crystal structure of mouse P5N-1 refined to 2.35 A resolution. The mouse P5N-1 has a 92% sequence identity to its human counterpart. The structure revealed that P5N-1 adopts a fold similar to enzymes of the haloacid dehydrogenase superfamily. The active site of this enzyme is structurally highly similar to those of phosphoserine phosphatases. We propose a catalytic mechanism for P5N-1 that is also similar to that of phosphoserine phosphatases and provide experimental evidence for the mechanism in the form of structures of several reaction cycle states, including: 1) P5N-1 with bound Mg(II) at 2.25 A, 2) phosphoenzyme intermediate analog at 2.30 A, 3) product-transition complex analog at 2.35 A, and 4) product complex at 2.1A resolution with phosphate bound in the active site. Furthermore the structure of Pb(II)-inhibited P5N-1 (at 2.35 A) revealed that Pb(II) binds within the active site in a way that compromises function of the cationic cavity, which is required for the recognition and binding of the phosphate group of nucleotides.

Selected figure(s)

Figure 2.
FIGURE 2. Comparison of mP5N-1 and its closest structural homolog. A, a stereo representation of structural superposition of mP5N-1 (red; Protein Data Bank code 2bdu) and hPSP (cyan; Protein Data Bank code 1l8o). Every 10th C[ ]carbon of mP5N-1 is highlighted by a red sphere, and some are labeled by residue numbers for better orientation. B, structural superposition of the active sites of mP5N-1 (red) and hPSP (cyan; Protein Data Bank code 1nnl).

Figure 3.
FIGURE 3. The reaction scheme of mP5N-1. A, mP5N-1 has two enzymatic activities: nucleotidase activity (steps 1 and 2a) and phosphotransferase activity (steps 1 and 2b). B, the proposed catalytic mechanism for nucleotidase activity of mP5N-1. "R" represents ribonucleoside. Individual states of the reaction mechanism include apoenzyme (I), active enzyme (II), the substrate complex (III), the substrate-transition complex (IV), the phosphoenzyme intermediate (V), the product-transition complex (VI), and the product complex (VII).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 20521-20529) copyright 2006.

Figures were selected by an automated process.