2AGW | pdb_00002agw

Crystal structure of tryptamine-reduced aromatic amine dehydrogenase (AADH) from Alcaligenes faecalis in complex with tryptamine

PDB DOI: https://doi.org/10.2210/pdb2AGW/pdb

Classification: OXIDOREDUCTASE
Organism(s): Alcaligenes faecalis
Mutation(s): No

Deposited: 2005-07-27 Released: 2006-04-25
Deposition Author(s): Masgrau, L., Roujeinikova, A., Johannissen, L.O., Hothi, P., Basran, J., Ranaghan, K.E., Mulholland, A.J., Sutcliffe, M.J., Scrutton, N.S., Leys, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.195 (Depositor), 0.197 (DCC)
R-Value Work:
0.163 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Atomic description of an enzyme reaction dominated by proton tunneling

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

(2006) Science 312: 237-241

PubMed: 16614214 Search on PubMed
DOI: https://doi.org/10.1126/science.1126002
Primary Citation Related Structures:
2AGL, 2AGW, 2AGX, 2AGY, 2AGZ, 2AH0, 2AH1

PubMed 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.

Organizational Affiliation

Manchester Interdisciplinary Biocentre, University of Manchester, Jackson's Mill, Post Office Box 88, Manchester M60 1QD, UK.

Macromolecule Content

Total Structure Weight: 109.38 kDa
Atom Count: 8,603
Modeled Residue Count: 949
Deposited Residue Count: 992
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic amine dehydrogenase	A [auth D], B [auth H]	135	Alcaligenes faecalis	Mutation(s): 0 EC: 1.4.99.4 (PDB Primary Data), 1.4.9.2 (UniProt)
UniProt
Find proteins for P84887 (Alcaligenes faecalis) Explore P84887 Go to UniProtKB: P84887
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84887
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic amine dehydrogenase	C [auth A], D [auth B]	361	Alcaligenes faecalis	Mutation(s): 0 EC: 1.4.99.4 (PDB Primary Data), 1.4.9.2 (UniProt)
UniProt
Find proteins for P84888 (Alcaligenes faecalis) Explore P84888 Go to UniProtKB: P84888
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84888
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TSS Query on TSS Download:Ideal Coordinates CCD File SDF format, chain E [auth D] SDF format, chain F [auth H] MOL2 format, chain E [auth D] MOL2 format, chain F [auth H] mmCIF format, chain E [auth D] mmCIF format, chain F [auth H]	E [auth D], F [auth H]	2-(1H-INDOL-3-YL)ETHANAMINE C₁₀ H₁₂ N₂ APJYDQYYACXCRM-UHFFFAOYSA-N		Interactions Focus chain E [auth D] Focus chain F [auth H] Interactions & Density Focus chain E [auth D] Focus chain F [auth H]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TQQ Query on TQQ	A [auth D], B [auth H]	L-PEPTIDE LINKING	C₁₁ H₁₁ N₃ O₃		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.195 (Depositor), 0.197 (DCC)
R-Value Work: 0.163 (Depositor), 0.165 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.998	α = 90
b = 88.749	β = 89.99
c = 81.149	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2006-04-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-04-25
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-16
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary