PDBsum entry 2ah0

Oxidoreductase

PDB id: 2ah0

Contents

Protein chains

109 a.a. *

360 a.a. *

Ligands

TSH

TSC

Waters ×1347

* Residue conservation analysis

PDB id:

2ah0

Name:

Oxidoreductase

Title:

Crystal structure of the carbinolamine intermediate in the reductive half-reaction of aromatic amine dehydrogenase (aadh) with tryptamine. Monoclinic form

Structure:

Aromatic amine dehydrogenase. Chain: d, h. Fragment: residues 48-182. Aromatic amine dehydrogenase. Chain: a, b. Fragment: residues 73-433. Ec: 1.4.99.4

Source:

Alcaligenes faecalis. Organism_taxid: 511. Strain: ifo 14479. Strain: ifo 14479

Biol. unit:

Tetramer (from PQS)

Resolution:

1.45Å R-factor: 0.169 R-free: 0.200

Authors:

L.Masgrau,A.Roujeinikova,L.O.Johannissen,P.Hothi,J.Basran, K.E.Ranaghan,A.J.Mulholland,M.J.Sutcliffe,N.S.Scrutton,D.Leys

Key ref:

L.Masgrau et al. (2006). Atomic description of an enzyme reaction dominated by proton tunneling. Science, 312, 237-241. PubMed id: 16614214 DOI: 10.1126/science.1126002

Date:

27-Jul-05 Release date: 25-Apr-06

Protein chains

P84887  (AAUA_ALCFA) -  Aralkylamine dehydrogenase light chain from Alcaligenes faecalis

Seq: 182 a.a.

Struc: 109 a.a.*

Protein chains

P84888  (AAUB_ALCFA) -  Aralkylamine dehydrogenase heavy chain from Alcaligenes faecalis

Seq: 390 a.a.

Struc: 360 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains D, H, A, B: E.C.1.4.9.2 - aralkylamine dehydrogenase (azurin).
• Reaction: an aralkylamine + 2 oxidized [azurin] + H2O = an aromatic aldehyde + 2 reduced [azurin] + NH4⁺ + 2 H⁺

aralkylamine + 2 × oxidized [azurin] + H2O = aromatic aldehyde (Bound ligand (Het Group name = TSC) matches with 61.54% similarity) + 2 × reduced [azurin] + NH4(+) + 2 × H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1126/science.1126002

Science 312:237-241 (2006)

PubMed id: 16614214

Atomic description of an enzyme reaction dominated by proton tunneling.

L.Masgrau, A.Roujeinikova, L.O.Johannissen, P.Hothi, J.Basran, K.E.Ranaghan, A.J.Mulholland, M.J.Sutcliffe, N.S.Scrutton, D.Leys.

ABSTRACT

We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp(128)beta in a reaction dominated by tunneling over approximately 0.6 angstroms. The role of long-range coupled motions in promoting tunneling is controversial. We show that, in this enzyme system, tunneling is promoted by a short-range motion modulating proton-acceptor distance and no long-range coupled motion is required.

Selected figure(s)

Figure 1.
Fig. 1. Schematic overview of the AADH reaction with tryptamine. The AADH structure is represented in cartoon form with the subunit in blue, the ß subunit in yellow, and the TTQ cofactor in magenta spheres. The reductive half-reaction with tryptamine is depicted in detail in Fig. 2. The oxidative half-reaction consists of two consecutive long-range electron transfer events to the single-electron carrier azurin. An azurin from Pseudomonas putida (PDB code 1NWO) is depicted in green cartoon with the copper atom as an orange sphere.

Figure 2.
Fig. 2. Reductive half-reaction of AADH with tryptamine. (A) Schematic overview of the proposed reaction mechanism. Intermediates are numbered by roman numerals; for clarity only key atoms are represented from intermediate II onward, whereas TTQ atoms C6 and C7 and Asp128ß O1 and O2 are labeled for intermediate I. Atoms derived from the substrate are depicted in magenta; those derived from water, in blue. All other enzyme-derived atoms are depicted in black. (B) AADH active site structure for the ligand-free protein, represented by atom-colored sticks: green carbons, TTQ cofactor; other carbons, yellow. The position occupied by the substrate in complex with the reduced AADH is depicted in dark gray, and the positions in intermediate V of substrate Leu179 and TTQ are in light gray; putative hydrogen bonds are shown as green dashed lines. (C) Active site and SigmaA weighted F[o]F[c] and 2F[o]F[c]-electron density of intermediates in the reductive half-reaction with tryptamine. Atoms are colored according to atom type, with substrate-derived carbon atoms in magenta and protein-derived carbon atoms in yellow. For clarity, only substrate- or inhibitor-derived atoms are shown, in addition to the side chain atoms for residues Asp128ß and Thr172ß and part of the TTQ cofactor. The 2F[o]F[c] density for these enzyme-derived atoms or water molecules is shown as a blue mesh, whereas F[o]F[c] density for the substrate- or inhibitor-derived atoms is depicted at 4 and shown as a magenta mesh. Intermediates are labeled by roman numerals corresponding to (A). The covalent phenylhydrazine-AADH complex is used as a model for intermediate III. For intermediate V, electron density for the P2[1] crystal form is shown, whereas intermediate VII is depicted by electron density for the F222 crystal form.

The above figures are reprinted by permission from the AAAs: Science (2006, 312, 237-241) copyright 2006.

Figures were selected by the author.