6ZXC | pdb_00006zxc

Diguanylate cyclase DgcR (I-site mutant) in activated state

PDB DOI: https://doi.org/10.2210/pdb6ZXC/pdb

Classification: SIGNALING PROTEIN
Organism(s): Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-07-29 Released: 2021-03-31
Deposition Author(s): Teixeira, R.D., Schirmer, T.
Funding Organization(s): Swiss National Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.288 (Depositor), 0.278 (DCC)
R-Value Work:
0.237 (Depositor), 0.227 (DCC)
R-Value Observed:
0.228 (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

Activation mechanism of a small prototypic Rec-GGDEF diguanylate cyclase.

Teixeira, R.D., Holzschuh, F., Schirmer, T.

(2021) Nat Commun 12: 2162-2162

PubMed: 33846343 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-021-22492-7
Primary Citation Related Structures:
6ZXB, 6ZXC, 6ZXM

PubMed Abstract:
Diguanylate cyclases synthesising the bacterial second messenger c-di-GMP are found to be regulated by a variety of sensory input domains that control the activity of their catalytical GGDEF domain, but how activation proceeds mechanistically is, apart from a few examples, still largely unknown. As part of two-component systems, they are activated by cognate histidine kinases that phosphorylate their Rec input domains. DgcR from Leptospira biflexa is a constitutively dimeric prototype of this class of diguanylate cyclases. Full-length crystal structures reveal that BeF ₃ ^- pseudo-phosphorylation induces a relative rotation of two rigid halves in the Rec domain. This is coupled to a reorganisation of the dimeric structure with concomitant switching of the coiled-coil linker to an alternative heptad register. Finally, the activated register allows the two substrate-loaded GGDEF domains, which are linked to the end of the coiled-coil via a localised hinge, to move into a catalytically competent dimeric arrangement. Bioinformatic analyses suggest that the binary register switch mechanism is utilised by many diguanylate cyclases with N-terminal coiled-coil linkers.

Organizational Affiliation

Structural Biology, Biozentrum, University of Basel, Basel, Switzerland.

Macromolecule Content

Total Structure Weight: 146.42 kDa
Atom Count: 9,529
Modeled Residue Count: 1,172
Deposited Residue Count: 1,272
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative GGDEF/response regulator receiver domain protein	A, B, C, D	318	Leptospira biflexa serovar Patoc strain 'Patoc 1 (Paris)	Mutation(s): 2 Gene Names: LEPBI_p0053 EC: 2.7.7.65
UniProt
Find proteins for B0SUI1 (Leptospira biflexa serovar Patoc (strain Patoc 1 / ATCC 23582 / Paris)) Explore B0SUI1 Go to UniProtKB: B0SUI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B0SUI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GH3 Query on GH3 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain R [auth D]	F [auth A], J [auth B], N [auth C], R [auth D]	3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ QGYIFQKZZSSUCR-OBXARNEKSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D]	E [auth A] G [auth A] H [auth A] I [auth B] K [auth B] E [auth A], G [auth A], H [auth A], I [auth B], K [auth B], L [auth B], M [auth C], O [auth C], P [auth C], Q [auth D], S [auth D], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Focus chain S [auth D] Focus chain T [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BFD Query on BFD	A, B, C, D	L-PEPTIDE LINKING	C₄ H₆ Be F₃ N O₄		ASP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.288 (Depositor), 0.278 (DCC)
R-Value Work: 0.237 (Depositor), 0.227 (DCC)
R-Value Observed: 0.228 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.812	α = 90
b = 247.368	β = 90
c = 41.539	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-03-31

Deposition Author(s):

Teixeira, R.D.

Schirmer, T.

Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	31003A-166652

Revision History (Full details and data files)

Version 1.0: 2021-03-31
Type: Initial release
Version 1.1: 2021-07-28
Changes: Database references
Version 1.2: 2024-01-31
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-09
Changes: Structure summary