PDBsum entry 4e4z

Oxidoreductase

PDB id: 4e4z

Contents

Protein chain

312 a.a.

Ligands

PEO

GOL ×4

Metals

_CU ×2

_NI

Waters ×149

PDB id:

4e4z

Name:

Oxidoreductase

Title:

Oxidized (cu2+) peptidylglycine alpha-hydroxylating monooxygenase (phm) in complex with hydrogen peroxide (1.98 a)

Structure:

Peptidyl-glycine alpha-amidating monooxygenase. Chain: a. Fragment: unp residues 45-356. Synonym: pam, peptidylglycine alpha-hydroxylating monooxygenase, phm, peptidyl-alpha-hydroxyglycine alpha-amidating lyase, peptidylamidoglycolate lyase, pal. Engineered: yes

Source:

Rattus norvegicus. Brown rat,rat,rats. Organism_taxid: 10116. Gene: pam. Expressed in: cricetulus griseus. Expression_system_taxid: 10029

Resolution:

1.98Å R-factor: 0.206 R-free: 0.244

Authors:

K.Rudzka,L.M.Amzel

Key ref:

K.Rudzka et al. (2013). Coordination of peroxide to the Cu(M) center of peptidylglycine α-hydroxylating monooxygenase (PHM): structural and computational study. J Biol Inorg Chem, 18, 223-232. PubMed id: 23247335

Date:

13-Mar-12 Release date: 23-Jan-13

Protein chain

P14925  (AMD_RAT) -  Peptidylglycine alpha-amidating monooxygenase from Rattus norvegicus

Seq: 976 a.a.

Struc: 312 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.14.17.3 - peptidylglycine monooxygenase.
• Reaction: a [peptide]-C-terminal glycine + 2 L-ascorbate + O2 = a [peptide]-C- terminal (2S)-2-hydroxyglycine + 2 monodehydro-L-ascorbate radical + H2O

[peptide]-C-terminal glycine + 2 × L-ascorbate (Bound ligand (Het Group name = GOL) matches with 50.00% similarity) + O2 (Bound ligand (Het Group name = PEO) corresponds exactly) = [peptide]-C- terminal (2S)-2-hydroxyglycine + 2 × monodehydro-L-ascorbate radical + H2O

• Cofactor: Cu cation
• Enzyme class 2: E.C.4.3.2.5 - peptidylamidoglycolate lyase.
• Reaction: a [peptide]-C-terminal (2S)-2-hydroxyglycine = a [peptide]-C-terminal amide + glyoxylate

[peptide]-C-terminal (2S)-2-hydroxyglycine = 2 × [peptide]-C-terminal amide + glyoxylate (Bound ligand (Het Group name = GOL) matches with 57.14% similarity)

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 Biol Inorg Chem 18:223-232 (2013)

PubMed id: 23247335

Coordination of peroxide to the Cu(M) center of peptidylglycine α-hydroxylating monooxygenase (PHM): structural and computational study.

K.Rudzka, D.M.Moreno, B.Eipper, R.Mains, D.A.Estrin, L.M.Amzel.

ABSTRACT

Many bioactive peptides, such as hormones and neuropeptides, require amidation at the C terminus for their full biological activity. Peptidylglycine α-hydroxylating monooxygenase (PHM) performs the first step of the amidation reaction-the hydroxylation of peptidylglycine substrates at the Cα position of the terminal glycine. The hydroxylation reaction is copper- and O(2)-dependent and requires 2 equiv of exogenous reductant. The proposed mechanism suggests that O(2) is reduced by two electrons, each provided by one of two nonequivalent copper sites in PHM (Cu(H) and Cu(M)). The characteristics of the reduced oxygen species in the PHM reaction and the identity of the reactive intermediate remain uncertain. To further investigate the nature of the key intermediates in the PHM cycle, we determined the structure of the oxidized form of PHM complexed with hydrogen peroxide. In this 1.98-Å-resolution structure (hydro)peroxide binds solely to Cu(M) in a slightly asymmetric side-on mode. The O-O interatomic distance of the copper-bound ligand is 1.5 Å, characteristic of peroxide/hydroperoxide species, and the Cu-O distances are 2.0 and 2.1 Å. Density functional theory calculations using the first coordination sphere of the Cu(M) active site as a model system show that the computed energies of the side-on L(3)Cu(M)(II)-O(2) (2-) species and its isomeric, end-on structure L(3)Cu(M)(I)-O(2) (·-) are similar, suggesting that both these intermediates are significantly populated within the protein environment. This observation has important mechanistic implications. The geometry of the observed side-on coordinated peroxide ligand in L(3)Cu(M)(II)O(2) (2-) is in good agreement with the results of a hybrid quantum mechanical-molecular mechanical optimization of this species.