PDBsum entry: 1pkx

Transferase, hydrolase

PDB id: 1pkx

Contents

Protein chains

588 a.a. *

Ligands

XMP ×2

Metals

__K ×4

Waters ×977

* Residue conservation analysis

PDB id:

1pkx

Name:

Transferase, hydrolase

Title:

Crystal structure of human atic in complex with xmp

Structure:

Bifunctional purine biosynthesis protein purh. Chain: a, b, c, d. Synonym: atic. Engineered: yes. Other_details: includes: phosphoribosylaminoimidazolecarboxamide formyltransferase (aicar transformylase) and imp cyclohydrolase (inosinicase) (imp synthetase)

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: atic. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.211 R-free: 0.249

Authors:

D.W.Wolan,C.G.Cheong,S.E.Greasley,I.A.Wilson

Key ref:

D.W.Wolan et al. (2004). Structural insights into the human and avian IMP cyclohydrolase mechanism via crystal structures with the bound XMP inhibitor. Biochemistry, 43, 1171-1183. PubMed id: 14756553 DOI: 10.1021/bi030162i

Date:

06-Jun-03 Release date: 17-Feb-04

Protein chains

P31939  (PUR9_HUMAN) -  Bifunctional purine biosynthesis protein PURH

Seq: 592 a.a.

Struc: 588 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.1.2.3 - Phosphoribosylaminoimidazolecarboxamide formyltransferase.
• Pathway: Purine Biosynthesis (late stages)
• Reaction: 10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamide = tetrahydrofolate + 5-formamido-1-(5-phospho-D- ribosyl)imidazole-4-carboxamide

10-formyltetrahydrofolate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamide = tetrahydrofolate + 5-formamido-1-(5-phospho-D- ribosyl)imidazole-4-carboxamide (Bound ligand (Het Group name = XMP) corresponds exactly)

• Enzyme class 3: E.C.3.5.4.10 - Imp cyclohydrolase.

Pathway:

• Reaction: IMP + H₂O = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide

IMP + H(2)O = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide (Bound ligand (Het Group name = XMP) corresponds exactly)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: mitochondrion (1 term)
• Biological process: nucleobase, nucleoside, nucleotide and nucleic acid metabolic process (5 terms)
• Biochemical function: catalytic activity (7 terms)

reference

DOI no: 10.1021/bi030162i

Biochemistry 43:1171-1183 (2004)

PubMed id: 14756553

Structural insights into the human and avian IMP cyclohydrolase mechanism via crystal structures with the bound XMP inhibitor.

D.W.Wolan, C.G.Cheong, S.E.Greasley, I.A.Wilson.

ABSTRACT

Within de novo purine biosynthesis, the AICAR transformylase and IMP cyclohydrolase activities of the bifunctional enzyme ATIC convert the intermediate AICAR to the final product of the pathway, IMP. Identification of the AICAR transformylase active site and a proposed formyl transfer mechanism have already resulted from analysis of crystal structures of avian ATIC in complex with substrate and/or inhibitors. Herein, we focus on the IMPCH active site and the cyclohydrolase mechanism through comparison of crystal structures of XMP inhibitor complexes of human ATIC at 1.9 A resolution with the previously determined avian enzyme. This first human ATIC structure was also determined to ascertain whether any subtle structural differences, compared to the homologous avian enzyme, should be taken into account for structure-based inhibitor design. These structural comparisons, as well as comparative analyses with other IMP and XMP binding proteins, have enabled a catalytic mechanism to be formulated. The primary role of the IMPCH active site appears to be to induce a reconfiguration of the substrate FAICAR to a less energetically favorable, but more reactive, conformer. Backbone (Arg64 and Lys66) and side chain interactions (Thr67) in the IMPCH active site reorient the 4-carboxamide from the preferred conformer that binds to the AICAR Tfase active site to one that promotes intramolecular cyclization. Other backbone amides (Ile126 and Gly127) create an oxyanion hole that helps orient the formyl group for nucleophilic attack by the 4-carboxamide amine and then stabilize the anionic intermediate. Several other residues, including Lys66, Tyr104, Asp125, and Lys137', provide substrate specificity and likely enhance the catalytic rate through contributions to acid-base catalysis.