4P99 | pdb_00004p99

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice

• PDB DOI: https://doi.org/10.2210/pdb4P99/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Marinomonas primoryensis
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2014-04-02 Released: 2014-06-18 
• Deposition Author(s): Guo, S., Vance, D.R.T., Campbell, R.L., Davies, P.L.
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice.

Vance, T.D., Olijve, L.L., Campbell, R.L., Voets, I.K., Davies, P.L., Guo, S.

(2014) Biosci Rep 34

• PubMed: 24892750 
• DOI: https://doi.org/10.1042/BSR20140083
• Primary Citation Related Structures: 
  4P99


• PubMed Abstract: 
  

  The large size of a 1.5-MDa ice-binding adhesin [MpAFP (Marinomonas primoryensis antifreeze protein)] from an Antarctic Gram-negative bacterium, M. primoryensis, is mainly due to its highly repetitive RII (Region II). MpAFP_RII contains roughly 120 tandem copies of an identical 104-residue repeat. We have previously determined that a single RII repeat folds as a Ca2+-dependent immunoglobulin-like domain. Here, we solved the crystal structure of RII tetra-tandemer (four tandem RII repeats) to a resolution of 1.8 Å. The RII tetra-tandemer reveals an extended (~190-Å × ~25-Å), rod-like structure with four RII-repeats aligned in series with each other. The inter-repeat regions of the RII tetra-tandemer are strengthened by Ca2+ bound to acidic residues. SAXS (small-angle X-ray scattering) profiles indicate the RII tetra-tandemer is significantly rigidified upon Ca2+ binding, and that the protein's solution structure is in excellent agreement with its crystal structure. We hypothesize that >600 Ca2+ help rigidify the chain of ~120 104-residue repeats to form a ~0.6 μm rod-like structure in order to project the ice-binding domain of MpAFP away from the bacterial cell surface. The proposed extender role of RII can help the strictly aerobic, motile bacterium bind ice in the upper reaches of the Antarctic lake where oxygen and nutrients are most abundant. Ca2+-induced rigidity of tandem Ig-like repeats in large adhesins might be a general mechanism used by bacteria to bind to their substrates and help colonize specific niches.

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Organizational Affiliation: 
• *Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
†Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 178.38 kDa 
• Atom Count: 13,555 
• Modeled Residue Count: 1,660 
• Deposited Residue Count: 1,748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MpAFP_RII tetra-tandemer	A, B, C, D	437	Marinomonas primoryensis	Mutation(s): 0
UniProt
Find proteins for A0A075B5G5 (Marinomonas primoryensis) Explore A0A075B5G5  Go to UniProtKB:  A0A075B5G5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	DC [auth C], QD [auth C], ZE [auth D]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
TRS	PD [auth C]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], GD [auth C], HA [auth A], HD [auth C], IA [auth A], ID [auth C], JA [auth A], JD [auth C], KB [auth B], KD [auth C], LA [auth A], LB [auth B], LD [auth C], MA [auth A], MB [auth B], MD [auth C], NB [auth B], ND [auth C], OB [auth B], OD [auth C], PB [auth B], QB [auth B], QE [auth D], RB [auth B], RD [auth D], RE [auth D], SB [auth B], SE [auth D], TB [auth B], TE [auth D], UB [auth B], UE [auth D], VB [auth B], VE [auth D], WB [auth B], WE [auth D], XB [auth B], XE [auth D], YB [auth B], YE [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	AA [auth A], AB [auth B], AC [auth B], AD [auth C], AE [auth D], BA [auth A], BB [auth B], BC [auth C], BD [auth C], BE [auth D], CB [auth B], CC [auth C], CD [auth C], CE [auth D], DB [auth B], DD [auth C], DE [auth D], E [auth A], EB [auth B], EC [auth C], ED [auth C], EE [auth D], F [auth A], FB [auth B], FC [auth C], FD [auth C], FE [auth D], G [auth A], GB [auth B], GC [auth C], GE [auth D], H [auth A], HB [auth B], HC [auth C], HE [auth D], I [auth A], IB [auth B], IC [auth C], IE [auth D], J [auth A], JB [auth B], JC [auth C], JE [auth D], K [auth A], KA [auth A], KC [auth C], KE [auth D], L [auth A], LC [auth C], LE [auth D], M [auth A], MC [auth C], ME [auth D], N [auth A], NA [auth B], NC [auth C], NE [auth D], O [auth A], OA [auth B], OC [auth C], OE [auth D], P [auth A], PA [auth B], PC [auth C], PE [auth D], Q [auth A], QA [auth B], QC [auth C], R [auth A], RA [auth B], RC [auth C], S [auth A], SA [auth B], SC [auth C], SD [auth D], T [auth A], TA [auth B], TC [auth C], TD [auth D], U [auth A], UA [auth B], UC [auth C], UD [auth D], V [auth A], VA [auth B], VC [auth C], VD [auth D], W [auth A], WA [auth B], WC [auth C], WD [auth D], X [auth A], XA [auth B], XC [auth C], XD [auth D], Y [auth A], YA [auth B], YC [auth C], YD [auth D], Z [auth A], ZA [auth B], ZB [auth B], ZC [auth C], ZD [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.257 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.464	α = 90.04
b = 47.469	β = 90.01
c = 191.161	γ = 90.02

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-06-18 
Deposition Author(s): Guo, S., Vance, D.R.T., Campbell, R.L., Davies, P.L.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	394878

Revision History  

• Version 1.0: 2014-06-18
  Type: Initial release
  
• Version 1.1: 2014-10-01
  Changes: Database references
• Version 1.2: 2015-02-04
  Changes: Derived calculations
• Version 1.3: 2020-01-08
  Changes: Advisory, Author supporting evidence, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Refinement description, Structure summary
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Structure summary