PDBsum entry 4fe3

Protein binding

PDB id: 4fe3

Contents

Protein chain

291 a.a.

Ligands

BME ×2

U5P

Metals

_NA

_MG

Waters ×335

PDB id:

4fe3

Name:

Protein binding

Title:

Structure of murine cytosolic 5'-nucleotidase iii complexed with uridinine monophosphate

Structure:

Cytosolic 5'-nucleotidase 3. Chain: a. Fragment: unp residues 42-327. Synonym: cytosolic 5'-nucleotidase iii, cn-iii, lupin, pyrimidine 5'- nucleotidase 1, p5'n-1, p5n-1, pn-i. Engineered: yes. Mutation: yes

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Gene: nt5c3, nt5c3_predicted, rcg_52382. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.74Å R-factor: 0.172 R-free: 0.219

Authors:

E.Bitto,C.A.Bingman

Key ref:

C.L.Grobosky et al. (2012). Structural basis of substrate specificity and selectivity of murine cytosolic 5'-nucleotidase III. J Mol Biol, 423, 540-554. PubMed id: 22925580

Date:

29-May-12 Release date: 29-Aug-12

Protein chain

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

Seq: 331 a.a.

Struc: 291 a.a.*

* PDB and UniProt seqs differ at 6 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

ribonucleoside 5'-phosphate + H2O = ribonucleoside (Bound ligand (Het Group name = U5P) matches with 40.91% similarity) + 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

CMP (Bound ligand (Het Group name = U5P) matches with 90.91% similarity) + 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

J Mol Biol 423:540-554 (2012)

PubMed id: 22925580

Structural basis of substrate specificity and selectivity of murine cytosolic 5'-nucleotidase III.

C.L.Grobosky, J.B.Lopez, S.Rennie, D.J.Skopelitis, A.T.Wiest, C.A.Bingman, E.Bitto.

ABSTRACT

Cytosolic 5'-nucleotidase III (cN-III) is responsible for selective degradation of pyrimidine 5'-monoribonucleotides during maturation of reticulocytes to erythrocytes. The lack of this enzymatic activity due to genetic aberrations or lead poisoning results in a mild to moderate nonspherocytic hemolytic anemia. In affected individuals, pyrimidine nucleotides as well as their precursor polymers and their off-path metabolites accumulate in erythrocytes, interfering with their proper function in ways that are not yet fully understood. This report describes the first X-ray structure of a catalytically inactivated variant of murine cN-III with a natural substrate, uridine 5'-monophosphate, in the active site at 1.74Å resolution. The structure captures in an atomic detail the closed conformation that cN-III adopts upon substrate binding. Structure and sequence analysis coupled with enzymatic characterization of several mutants confirmed that the aromatic ring of a nitrogenous base of substrate nucleotide is stabilized by parallel π-stacking interactions with conserved aromatic rings of Trp113 and His68. The nitrogenous base is further stabilized by T-shaped stacking with the conserved aromatic ring of Tyr114, as well as by polar contacts with side chains of Thr66 and Ser117. Two water molecules help to stabilize the nucleotide binding by bridging it to protein residues Asp72 and His68 via hydrogen bonds. Finally, fully conserved Glu96 is responsible for recognition of ribose ring via two hydrogen bonds. The presented substrate complex structure elucidates how cN-III achieves specificity for pyrimidine 5'-nucleotides and how it selects against purine 5'-nucleotides.