4RV7 | pdb_00004rv7

Characterization of an essential diadenylate cyclase

PDB DOI: https://doi.org/10.2210/pdb4RV7/pdb

Classification: TRANSFERASE
Organism(s): Listeria monocytogenes EGD-e
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-25 Released: 2015-01-28
Deposition Author(s): Dickmanns, A., Neumann, P., Ficner, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.256 (Depositor), 0.261 (DCC)
R-Value Work:
0.240 (Depositor), 0.244 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structural and Biochemical Analysis of the Essential Diadenylate Cyclase CdaA from Listeria monocytogenes.

Rosenberg, J., Dickmanns, A., Neumann, P., Gunka, K., Arens, J., Kaever, V., Stulke, J., Ficner, R., Commichau, F.M.

(2015) J Biological Chem 290: 6596-6606

PubMed: 25605729 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.M114.630418
Primary Citation Related Structures:
4RV7

PubMed Abstract:
The recently identified second messenger cyclic di-AMP (c-di-AMP) is involved in several important cellular processes, such as cell wall metabolism, maintenance of DNA integrity, ion transport, transcription regulation, and allosteric regulation of enzyme function. Interestingly, c-di-AMP is essential for growth of the Gram-positive model bacterium Bacillus subtilis. Although the genome of B. subtilis encodes three c-di-AMP-producing diadenlyate cyclases that can functionally replace each other, the phylogenetically related human pathogens like Listeria monocytogenes and Staphylococcus aureus possess only one enzyme, the diadenlyate cyclase CdaA. Because CdaA is also essential for growth of these bacteria, the enzyme is a promising target for the development of novel antibiotics. Here we present the first crystal structure of the L. monocytogenes CdaA diadenylate cyclase domain that is conserved in many human pathogens. Moreover, biochemical characterization of the cyclase revealed an unusual metal cofactor requirement.

Organizational Affiliation

From the Departments of General Microbiology and.

Macromolecule Content

Total Structure Weight: 86.25 kDa
Atom Count: 4,991
Modeled Residue Count: 633
Deposited Residue Count: 768
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Diadenylate cyclase	A, B, C, D	192	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: dacA, lmo2120 EC: 2.7.7.85
UniProt
Find proteins for Q8Y5E4 (Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)) Explore Q8Y5E4 Go to UniProtKB: Q8Y5E4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8Y5E4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	E [auth A], H [auth B], J [auth C], L [auth D]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]
HEZ Query on HEZ Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D]	F [auth A], I [auth B], K [auth C], M [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.256 (Depositor), 0.261 (DCC)
R-Value Work: 0.240 (Depositor), 0.244 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.68	α = 90
b = 130.68	β = 90
c = 178.15	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-01-28

Deposition Author(s):

Dickmanns, A.

Neumann, P.

Ficner, R.

Revision History (Full details and data files)

Version 1.0: 2015-01-28
Type: Initial release
Version 1.1: 2015-03-25
Changes: Database references
Version 1.2: 2018-03-07
Changes: Data collection
Version 1.3: 2019-09-04
Changes: Data collection
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description