SASDGN5: apo-RD domain of B. Pertussis Adenylate Cyclase Toxin (CyaA)

Basic information

• Entry: Database: SASBDB / ID: SASDGN5

Sample

apo-RD domain of B. Pertussis Adenylate Cyclase Toxin (CyaA)

• RD domain of B. Pertussis Adenylate Cyclase Toxin (CyaA) (protein), RD domain of CyaA, Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)

Function / homology

Function:

calcium- and calmodulin-responsive adenylate cyclase activity / hemolysis in another organism / adenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / channel activity / positive regulation of cytosolic calcium ion concentration / toxin activity / calmodulin binding / calcium ion binding / host cell plasma membrane / extracellular region / ATP binding / membrane

Domain/homology:

RTX, pore-forming domain / N-terminal domain in RTX protein / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal

Component:

Bifunctional hemolysin/adenylate cyclase

• Biological species: Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251) (bacteria)
• Citation: Journal: Sci Rep / Year: 2015; Title: Structural models of intrinsically disordered and calcium-bound folded states of a protein adapted for secretion.; Authors: Darragh P O'Brien / Belen Hernandez / Dominique Durand / Véronique Hourdel / Ana-Cristina Sotomayor-Pérez / Patrice Vachette / Mahmoud Ghomi / Julia Chamot-Rooke / Daniel Ladant / Sébastien Brier / Alexandre Chenal / ; Abstract: Many Gram-negative bacteria use Type I secretion systems, T1SS, to secrete virulence factors that contain calcium-binding Repeat-in-ToXin (RTX) motifs. Here, we present structural models of an RTX protein, RD, in both its intrinsically disordered calcium-free Apo-state and its folded calcium-bound Holo-state. Apo-RD behaves as a disordered polymer chain comprising several statistical elements that exhibit local rigidity with residual secondary structure. Holo-RD is a folded multi-domain protein with an anisometric shape. RTX motifs thus appear remarkably adapted to the structural and mechanistic constraints of the secretion process. In the low calcium environment of the bacterial cytosol, Apo-RD is an elongated disordered coil appropriately sized for transport through the narrow secretion machinery. The progressive folding of Holo-RD in the extracellular calcium-rich environment as it emerges form the T1SS may then favor its unidirectional export through the secretory channel. This process is relevant for hundreds of bacterial species producing virulent RTX proteins.

Contact author

• Dominique DURAND (I2BC-CNRS, Paris, France)

Models

• Model #3789: ; Type: atomic / Chi-square value: 1.959; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: apo-RD domain of B. Pertussis Adenylate Cyclase Toxin (CyaA); Specimen concentration: 8 mg/ml
• Buffer: Name: 20 mM Hepes, 150 mM NaCl, 2 mM DTT / pH: 7.5

Entity #1895

Name: RD domain of CyaA / Type: protein
Description: RD domain of B. Pertussis Adenylate Cyclase Toxin (CyaA)
Formula weight: 72.62 / Num. of mol.: 1
Source: Bordetella pertussis (strain Tohama I / ATCC BAA-589 / NCTC 13251)
References: UniProt: P0DKX7
Sequence:

MLEHVQHIIG GAGNDSITGN AHDNFLAGGS GDDRLDGGAG NDTLVGGEGQ NTVIGGAGDD VFLQDLGVWS NQLDGGAGVD TVKYNVHQPS EERLERMGDT GIHADLQKGT VEKWPALNLF SVDHVKNIEN LHGSRLNDRI AGDDQDNELW GHDGNDTIRG RGGDDILRGG LGLDTLYGED GNDIFLQDDE TVSDDIDGGA GLDTVDYSAM IHPGRIVAPH EYGFGIEADL SREWVRKASA LGVDYYDNVR NVENVIGTSM KDVLIGDAQA NTLMGQGGDD TVRGGDGDDL LFGGDGNDML YGDAGNDTLY GGLGDDTLEG GAGNDWFGQT QAREHDVLRG GDGVDTVDYS QTGAHAGIAA GRIGLGILAD LGAGRVDKLG EAGSSAYDTV SGIENVVGTE LADRITGDAQ ANVLRGAGGA DVLAGGEGDD VLLGGDGDDQ LSGDAGRDRL YGEAGDDWFF QDAANAGNLL DGGDGRDTVD FSGPGRGLDA GAKGVFLSLG KGFASLMDEP ETSNVLRNIE NAVGSARDDV LIGDAGANVL NGLAGNDVLS GGAGDDVLLG DEGSDLLSGD AGNDDLFGGQ GDDTYLFGVG YGHDTIYESG GGHDTIRINA GADQLWFARQ GNDLEIRILG TDDALTVHDW YRDADHRVEI IHAANQAVDQ AGIEKLVEAM AQYPDPGAAA AAPPAARVPD TLMQSLAVNW R

Experimental information

• Beam: Instrument name: SOLEIL SWING / City: Saint-Aubin / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.1033 Å / Dist. spec. to detc.: 1.81 mm
• Detector: Name: AVIEX PCCD170170 / Type: CCD

Scan

Title: apo-RD domain of B. Pertussis Adenylate Cyclase Toxin (CyaA)
Measurement date: May 31, 2012 / Storage temperature: 10 °C / Cell temperature: 15 °C / Exposure time: 1 sec. / Number of frames: 250 / Unit: 1/A /

	Min	Max
Q	0.0056	0.4001

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 522 /

	Min	Max
Q	0.00620922	0.300026
P(R) point	1	522
R	0	330

Result

Type of curve: sec
Comments: The scattered intensities were displayed on an absolute scale (cm-1) using the scattering of water. Frames were examined individually and 61 identical frames obtained around the maximum of the elution peak were averaged and further processed. The corresponding concentration was 0.95g/L. The model ensemble of the apo-RD and the final fit to the SAXS pattern (blue dots) was performed using GAJOE analysis. The fit (red line) is the average scattering pattern of the seven conformations shown in the right panel.

	Experimental	Standard	Standard error
MW	70.5 kDa	70.5 kDa	7

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	0.059	0.0002	0.0588	0.0002
Radius of gyration, Rg	8.53 nm	1	8.27 nm	0.1

	Min	Max	Error
D	-	33	1.5
Guinier point	2	12	-