6HVL | pdb_00006hvl

CdaA complex with c-di-AMP and AMP

PDB DOI: https://doi.org/10.2210/pdb6HVL/pdb

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

Deposited: 2018-10-11 Released: 2019-06-05
Deposition Author(s): Heidemann, J.L., Neumann, P., Ficner, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.234 (Depositor), 0.212 (DCC)
R-Value Work:
0.188 (Depositor)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structures of the c-di-AMP-synthesizing enzyme CdaA.

Heidemann, J.L., Neumann, P., Dickmanns, A., Ficner, R.

(2019) J Biological Chem 294: 10463-10470

PubMed: 31118276 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1074/jbc.RA119.009246
Primary Citation Related Structures:
6HVL, 6HVM, 6HVN

PubMed Abstract:
Cyclic di-AMP (c-di-AMP) is the only second messenger known to be essential for bacterial growth. It has been found mainly in Gram-positive bacteria, including pathogenic bacteria like Listeria monocytogenes CdaA is the sole diadenylate cyclase in L. monocytogenes , making this enzyme an attractive target for the development of novel antibiotic compounds. Here we report crystal structures of CdaA from L. monocytogenes in the apo state, in the post-catalytic state with bound c-di-AMP and catalytic Co ²⁺ ions, as well as in a complex with AMP. These structures reveal the flexibility of a tyrosine side chain involved in locking the adenine ring after ATP binding. The essential role of this tyrosine was confirmed by mutation to Ala, leading to drastic loss of enzymatic activity.

Organizational Affiliation

From the Department of Molecular Structural Biology, Institute for Microbiology and Genetics, Göttingen Center for Molecular Biosciences, Georg-August-University Göttingen, 37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 39.9 kDa
Atom Count: 2,467
Modeled Residue Count: 312
Deposited Residue Count: 356
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	178	Listeria monocytogenes EGD-e	Mutation(s): 0 Gene Names: dacA, cdaA, 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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2BA Query on 2BA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide C₂₀ H₂₄ N₁₀ O₁₂ P₂ PDXMFTWFFKBFIN-XPWFQUROSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain F [auth B] MOL2 format, chain F [auth B] mmCIF format, chain F [auth B]	F [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CO Query on CO Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.234 (Depositor), 0.212 (DCC)
R-Value Work: 0.188 (Depositor)
R-Value Observed: 0.190 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.9	α = 90
b = 121.9	β = 90
c = 141.16	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-05

Deposition Author(s):

Heidemann, J.L.

Neumann, P.

Ficner, R.

Funding Organization	Location	Grant Number
	Germany	--

Revision History (Full details and data files)

Version 1.0: 2019-06-05
Type: Initial release
Version 1.1: 2019-07-17
Changes: Data collection, Database references
Version 1.2: 2019-11-20
Changes: Derived calculations
Version 1.3: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary