3RG2

Structure of a two-domain NRPS fusion protein containing the EntE adenylation domain and EntB aryl-carrier protein from enterobactin biosynthesis

PDB DOI: https://doi.org/10.2210/pdb3RG2/pdb

Classification: LIGASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-04-07 Released: 2012-03-07
Deposition Author(s): Sundlov, J.A., Gulick, A.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 ?
R-Value Free: 0.264
R-Value Work: 0.218
R-Value Observed: 0.220

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structural and Functional Investigation of the Intermolecular Interaction between NRPS Adenylation and Carrier Protein Domains.

Sundlov, J.A., Shi, C., Wilson, D.J., Aldrich, C.C., Gulick, A.M.

(2012) Chem Biol 19: 188-198

PubMed: 22365602 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1016/j.chembiol.2011.11.013
Primary Citation of Related Structures:
3RG2

PubMed Abstract:
Nonribosomal peptide synthetases (NRPSs) are modular proteins that produce peptide antibiotics and siderophores. These enzymes act as catalytic assembly lines where substrates, covalently bound to integrated carrier domains, are delivered to adjacent catalytic domains. The carrier domains are initially loaded by adenylation domains, which use two distinct conformations to catalyze sequentially the adenylation of the substrate and the thioesterification of the pantetheine cofactor. We have used?a mechanism-based inhibitor to determine the crystal structure of an engineered adenylation-carrier domain protein illustrating the intermolecular interaction between the adenylation and carrier domains. This structure enabled directed mutations to improve the interaction between nonnative partner proteins. Comparison with prior NRPS adenylation domain structures provides insights into the assembly line dynamics of these modular enzymes.

Organizational Affiliation

Hauptman-Woodward Institute and Department of Structural Biology, University at Buffalo, Buffalo, NY 14203 USA.

Macromolecule Content

Total Structure Weight: 694.56 kDa
Atom Count: 45,112
Modelled Residue Count: 6,078
Deposited Residue Count: 6,170
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Enterobactin synthase component E (entE), 2,3-dihydro-2,3-dihydroxybenzoate synthetase, isochroismatase (Entb)	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	617	Escherichia coli	Mutation(s): 0 Gene Names: b0594, entE, entE and entB, JW0586 EC: 2.7.7.58 (PDB Primary Data), 2.3.1 (PDB Primary Data), 3.3.2.1 (UniProt), 6.2.1.71 (UniProt), 6.3.2.14 (UniProt)
UniProt
Find proteins for P0ADI4 (Escherichia coli (strain K12)) Explore P0ADI4 Go to UniProtKB: P0ADI4
Find proteins for P10378 (Escherichia coli (strain K12)) Explore P10378 Go to UniProtKB: P10378
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ADI4P10378
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SVS Query on SVS Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain GA [auth E] SDF format, chain K [auth A] SDF format, chain LA [auth F] SDF format, chain OA [auth G] SDF format, chain Q [auth B] SDF format, chain RA [auth H] SDF format, chain UA [auth I] SDF format, chain X [auth C] SDF format, chain ZA [auth J] MOL2 format, chain AA [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth H] MOL2 format, chain UA [auth I] MOL2 format, chain X [auth C] MOL2 format, chain ZA [auth J] mmCIF format, chain AA [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth F] mmCIF format, chain OA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth H] mmCIF format, chain UA [auth I] mmCIF format, chain X [auth C] mmCIF format, chain ZA [auth J]	AA [auth D] GA [auth E] K [auth A] LA [auth F] OA [auth G] AA [auth D], GA [auth E], K [auth A], LA [auth F], OA [auth G], Q [auth B], RA [auth H], UA [auth I], X [auth C], ZA [auth J]	5'-deoxy-5'-({[2-(2-hydroxyphenyl)ethyl]sulfonyl}amino)adenosine C₁₈ H₂₂ N₆ O₆ S NIEGSPNRJDKALY-SCFUHWHPSA-N		Interactions Focus chain AA [auth D] Focus chain GA [auth E] Focus chain K [auth A] Focus chain LA [auth F] Focus chain OA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain UA [auth I] Focus chain X [auth C] Focus chain ZA [auth J] Interactions & Density Focus chain AA [auth D] Focus chain GA [auth E] Focus chain K [auth A] Focus chain LA [auth F] Focus chain OA [auth G] Focus chain Q [auth B] Focus chain RA [auth H] Focus chain UA [auth I] Focus chain X [auth C] Focus chain ZA [auth J]
PNS Query on PNS Download Ideal Coordinates CCD File SDF format, chain AB [auth J] SDF format, chain BA [auth D] SDF format, chain HA [auth E] SDF format, chain L [auth A] SDF format, chain MA [auth F] SDF format, chain PA [auth G] SDF format, chain R [auth B] SDF format, chain SA [auth H] SDF format, chain VA [auth I] SDF format, chain Y [auth C] MOL2 format, chain AB [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth F] MOL2 format, chain PA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth H] MOL2 format, chain VA [auth I] MOL2 format, chain Y [auth C] mmCIF format, chain AB [auth J] mmCIF format, chain BA [auth D] mmCIF format, chain HA [auth E] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth F] mmCIF format, chain PA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth H] mmCIF format, chain VA [auth I] mmCIF format, chain Y [auth C]	AB [auth J] BA [auth D] HA [auth E] L [auth A] MA [auth F] AB [auth J], BA [auth D], HA [auth E], L [auth A], MA [auth F], PA [auth G], R [auth B], SA [auth H], VA [auth I], Y [auth C]	4'-PHOSPHOPANTETHEINE C₁₁ H₂₃ N₂ O₇ P S JDMUPRLRUUMCTL-VIFPVBQESA-N		Interactions Focus chain AB [auth J] Focus chain BA [auth D] Focus chain HA [auth E] Focus chain L [auth A] Focus chain MA [auth F] Focus chain PA [auth G] Focus chain R [auth B] Focus chain SA [auth H] Focus chain VA [auth I] Focus chain Y [auth C] Interactions & Density Focus chain AB [auth J] Focus chain BA [auth D] Focus chain HA [auth E] Focus chain L [auth A] Focus chain MA [auth F] Focus chain PA [auth G] Focus chain R [auth B] Focus chain SA [auth H] Focus chain VA [auth I] Focus chain Y [auth C]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain BB [auth J] SDF format, chain CA [auth D] SDF format, chain CB [auth J] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain IA [auth E] SDF format, chain JA [auth E] SDF format, chain KA [auth E] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain NA [auth F] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth G] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth H] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth I] SDF format, chain XA [auth I] SDF format, chain YA [auth I] SDF format, chain Z [auth C] MOL2 format, chain BB [auth J] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth J] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain IA [auth E] MOL2 format, chain JA [auth E] MOL2 format, chain KA [auth E] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth G] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth I] MOL2 format, chain YA [auth I] MOL2 format, chain Z [auth C] mmCIF format, chain BB [auth J] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth J] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain IA [auth E] mmCIF format, chain JA [auth E] mmCIF format, chain KA [auth E] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth G] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth H] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth I] mmCIF format, chain XA [auth I] mmCIF format, chain YA [auth I] mmCIF format, chain Z [auth C]	BB [auth J] CA [auth D] CB [auth J] DA [auth D] EA [auth D] BB [auth J], CA [auth D], CB [auth J], DA [auth D], EA [auth D], FA [auth D], IA [auth E], JA [auth E], KA [auth E], M [auth A], N [auth A], NA [auth F], O [auth A], P [auth A], QA [auth G], S [auth B], T [auth B], TA [auth H], U [auth B], V [auth B], W [auth B], WA [auth I], XA [auth I], YA [auth I], Z [auth C]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain BB [auth J] Focus chain CA [auth D] Focus chain CB [auth J] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth G] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth H] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth I] Focus chain XA [auth I] Focus chain YA [auth I] Focus chain Z [auth C] Interactions & Density Focus chain BB [auth J] Focus chain CA [auth D] Focus chain CB [auth J] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain IA [auth E] Focus chain JA [auth E] Focus chain KA [auth E] Focus chain M [auth A] Focus chain N [auth A] Focus chain NA [auth F] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth G] Focus chain S [auth B] Focus chain T [auth B] Focus chain TA [auth H] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth I] Focus chain XA [auth I] Focus chain YA [auth I] Focus chain Z [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
SVS	PDBBind: 3RG2	Kd: 6.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 ?
R-Value Free: 0.264
R-Value Work: 0.218
R-Value Observed: 0.220
Space Group: P 1 2₁ 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 160.575	α = 90
b = 101.771	β = 107.06
c = 240.678	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
BALBES	phasing
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-07

Deposition Author(s):

Sundlov, J.A.

Gulick, A.M.

Revision History (Full details and data files)

Version 1.0: 2012-03-07
Type: Initial release
Version 1.1: 2012-03-28
Changes: Database references
Version 1.2: 2017-08-09
Changes: Refinement description, Source and taxonomy
Version 1.3: 2019-07-17
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2019-08-14
Changes: Data collection
Version 1.5: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description