4P99

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • DOI: 10.1042/BSR20140083
  • Primary Citation of 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 ...

    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.


    Organizational Affiliation

    *Protein Function Discovery Group and the Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MpAFP_RII tetra-tandemerA, B, C, D437Marinomonas primoryensisMutation(s): 0 
UniProt
Find proteins for A0A075B5G5 (Marinomonas primoryensis)
Explore A0A075B5G5 
Go to UniProtKB:  A0A075B5G5
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BOG (Subject of Investigation/LOI)
Query on BOG

Download Ideal Coordinates CCD File 
DC [auth C], QD [auth C], ZE [auth D]octyl beta-D-glucopyranoside
C14 H28 O6
HEGSGKPQLMEBJL-RKQHYHRCSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
PD [auth C]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth A] , DA [auth A] , EA [auth A] , FA [auth A] , GA [auth A] , GD [auth C] , HA [auth A] , HD [auth C] , 
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
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth A] , AB [auth B] , AC [auth B] , AD [auth C] , AE [auth D] , BA [auth A] , BB [auth B] , BC [auth C] , 
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
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.222 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.464α = 90.04
b = 47.469β = 90.01
c = 191.161γ = 90.02
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada394878

Revision History  (Full details and data files)

  • 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