5L7P

In silico-powered specific incorporation of photocaged Dopa at multiple protein sites

PDB DOI: https://doi.org/10.2210/pdb5L7P/pdb

Classification: LIGASE
Organism(s): Methanocaldococcus jannaschii DSM 2661
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-06-03 Released: 2017-09-13
Deposition Author(s): Hauf, M., Richter, F., Schneider, T., Martins, B.M., Baumann, T., Durkin, P., Dobbek, H., Moeglich, A., Budisa, N.
Funding Organization(s): Beilstein-Institut zur Foerderung der Chemischen Wissenschaften

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218
R-Value Work: 0.178
R-Value Observed: 0.180

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Photoactivatable Mussel-Based Underwater Adhesive Proteins by an Expanded Genetic Code.

Hauf, M., Richter, F., Schneider, T., Faidt, T., Martins, B.M., Baumann, T., Durkin, P., Dobbek, H., Jacobs, K., Moglich, A., Budisa, N.

(2017) Chembiochem 18: 1819-1823

PubMed: 28650092 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201700327
Primary Citation of Related Structures:
5L7P

PubMed Abstract:
Marine mussels exhibit potent underwater adhesion abilities under hostile conditions by employing 3,4-dihydroxyphenylalanine (DOPA)-rich mussel adhesive proteins (MAPs). However, their recombinant production is a major biotechnological challenge. Herein, a novel strategy based on genetic code expansion has been developed by engineering efficient aminoacyl-transfer RNA synthetases (aaRSs) for the photocaged noncanonical amino acid ortho-nitrobenzyl DOPA (ONB-DOPA). The engineered ONB-DOPARS enables in vivo production of MAP type 5 site-specifically equipped with multiple instances of ONB-DOPA to yield photocaged, spatiotemporally controlled underwater adhesives. Upon exposure to UV light, these proteins feature elevated wet adhesion properties. This concept offers new perspectives for the production of recombinant bioadhesives.

Organizational Affiliation

Institut für Chemie, Technische Universität Berlin, Müller-Breslau-Strasse 10, 10623, Berlin, Germany.

Macromolecule Content

Total Structure Weight: 73.38 kDa
Atom Count: 5,265
Modelled Residue Count: 607
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine--tRNA ligase	A, B	318	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 10 Gene Names: tyrS, MJ0389 EC: 6.1.1.1
UniProt
Find proteins for Q57834 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57834 Go to UniProtKB: Q57834
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q57834
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BUU Query on BUU Download Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B]	F [auth B]	(2~{S})-2-azanyl-3-[3-[(2-nitrophenyl)methoxy]-4-oxidanyl-phenyl]propanoic acid C₁₆ H₁₆ N₂ O₆ NKOMHGJPHGNQSO-LBPRGKRZSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.218
R-Value Work: 0.178
R-Value Observed: 0.180
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.507	α = 90
b = 78.275	β = 90
c = 137.883	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-09-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Beilstein-Institut zur Foerderung der Chemischen Wissenschaften	Germany	--

Revision History (Full details and data files)

Version 1.0: 2017-09-13
Type: Initial release
Version 1.1: 2017-09-27
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description