4H2X | pdb_00004h2x

Crystal structure of engineered Bradyrhizobium japonicum glycine:[carrier protein] ligase complexed with carrier protein from Agrobacterium tumefaciens and an analogue of glycyl adenylate

PDB DOI: https://doi.org/10.2210/pdb4H2X/pdb

Classification: LIGASE
Organism(s): Bradyrhizobium diazoefficiens USDA 110, Agrobacterium fabrum str. C58
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-09-13 Released: 2013-03-06
Deposition Author(s): Luic, M., Weygand-Durasevic, I., Ivic, N., Mocibob, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.198 (Depositor), 0.199 (DCC)
R-Value Work:
0.167 (Depositor), 0.171 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Adaptation of aminoacyl-tRNA synthetase catalytic core to carrier protein aminoacylation.

Mocibob, M., Ivic, N., Luic, M., Weygand-Durasevic, I.

(2013) Structure 21: 614-626

PubMed: 23541895 Search on PubMed
DOI: https://doi.org/10.1016/j.str.2013.02.017
Primary Citation Related Structures:
4H2S, 4H2T, 4H2U, 4H2V, 4H2W, 4H2X, 4H2Y

PubMed Abstract:
Amino acid:[carrier protein] ligases (aa:CP ligases) are recently discovered enzymes that are highly similar to class II aminoacyl-tRNA synthetases (aaRSs). However, while aaRSs aminoacylate tRNA and supply building blocks for ribosomal translation, aa:CP ligases transfer activated amino acids to the phosphopantetheine group of small carrier proteins. We have solved the crystal structure of an aa:CP ligase complexed with the carrier protein (CP). The CP prosthetic group enters the active site from a different direction than tRNA in class II aaRS complexes through an idiosyncratic tunnel. CP binds to aa:CP ligase in a fundamentally different manner compared to tRNA binding by structurally closely related aaRSs. Based on crystallographic analysis, an enzyme of altered CP specificity was designed, and the mechanism of amino acid transfer to the prosthetic group was proposed. The presented study reveals how a conserved class II aaRS catalytic core can adapt to another function through minor structural alterations.

Organizational Affiliation

Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10 000 Zagreb, Croatia.

Macromolecule Content

Total Structure Weight: 100.37 kDa
Atom Count: 6,243
Modeled Residue Count: 743
Deposited Residue Count: 898
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid--[acyl-carrier-protein] ligase 1	A	346	Bradyrhizobium diazoefficiens USDA 110, Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: bll0957, Atu2573, AGR_C_4663 EC: 6.2.1
UniProt
Find proteins for Q89VT8 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89VT8 Go to UniProtKB: Q89VT8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89VT8
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Amino acid--[acyl-carrier-protein] ligase 1	B	346	Bradyrhizobium diazoefficiens USDA 110, Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: bll0957, Atu2573, AGR_C_4663 EC: 6.2.1
UniProt
Find proteins for Q89VT8 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89VT8 Go to UniProtKB: Q89VT8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q89VT8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminoacyl carrier protein	C, D	103	Agrobacterium fabrum str. C58	Mutation(s): 0 Gene Names: AGR_C_4658, Atu2571
UniProt
Find proteins for A9CHM9 (Agrobacterium fabrum (strain C58 / ATCC 33970)) Explore A9CHM9 Go to UniProtKB: A9CHM9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9CHM9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
G5A Query on G5A Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	5'-O-(glycylsulfamoyl)adenosine C₁₂ H₁₇ N₇ O₇ S AMWPZASLDLLQFT-JJNLEZRASA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
PNS Query on PNS Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain K [auth D]	J [auth C], K [auth D]	4'-PHOSPHOPANTETHEINE C₁₁ H₂₃ N₂ O₇ P S JDMUPRLRUUMCTL-VIFPVBQESA-N		Interactions Focus chain J [auth C] Focus chain K [auth D] Interactions & Density Focus chain J [auth C] Focus chain K [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.198 (Depositor), 0.199 (DCC)
R-Value Work: 0.167 (Depositor), 0.171 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.575	α = 90
b = 101.433	β = 90
c = 103.044	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-03-06

Deposition Author(s):

Luic, M.

Weygand-Durasevic, I.

Ivic, N.

Mocibob, M.

Revision History (Full details and data files)

Version 1.0: 2013-03-06
Type: Initial release
Version 1.1: 2013-04-10
Changes: Database references
Version 1.2: 2013-05-29
Changes: Database references
Version 1.3: 2013-06-19
Changes: Atomic model
Version 1.4: 2017-08-23
Changes: Refinement description, Source and taxonomy
Version 1.5: 2025-03-26
Changes: Data collection, Database references, Derived calculations, Structure summary