5B5X | pdb_00005b5x

Crystal structure of limiting CO2-inducible protein LCIC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.283 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.220 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5B5X

This is version 1.2 of the entry. See complete history

Literature

Structural insights into the LCIB protein family reveals a new group of beta-carbonic anhydrases

Jin, S.Sun, J.Wunder, T.Tang, D.Cousins, A.B.Sze, S.K.Mueller-Cajar, O.Gao, Y.G.

(2016) Proc Natl Acad Sci U S A 113: 14716-14721

  • DOI: https://doi.org/10.1073/pnas.1616294113
  • Primary Citation Related Structures: 
    5B5X, 5B5Y, 5B5Z, 5B60, 5K5W

  • PubMed Abstract: 

    Aquatic microalgae have evolved diverse CO 2 -concentrating mechanisms (CCMs) to saturate the carboxylase with its substrate, to compensate for the slow kinetics and competing oxygenation reaction of the key photosynthetic CO 2 -fixing enzyme rubisco. The limiting CO 2 -inducible B protein (LCIB) is known to be essential for CCM function in Chlamydomonas reinhardtii To assign a function to this previously uncharacterized protein family, we purified and characterized a phylogenetically diverse set of LCIB homologs. Three of the six homologs are functional carbonic anhydrases (CAs). We determined the crystal structures of LCIB and limiting CO 2 -inducible C protein (LCIC) from C. reinhardtii and a CA-functional homolog from Phaeodactylum tricornutum, all of which harbor motifs bearing close resemblance to the active site of canonical β-CAs. Our results identify the LCIB family as a previously unidentified group of β-CAs, and provide a biochemical foundation for their function in the microalgal CCMs.


  • Organizational Affiliation
    • School of Biological Sciences, Nanyang Technological University, Singapore 637551.

Macromolecule Content 

  • Total Structure Weight: 33.42 kDa 
  • Atom Count: 1,734 
  • Modeled Residue Count: 225 
  • Deposited Residue Count: 308 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
limiting CO2-inducible protein LCIC308Chlamydomonas reinhardtiiMutation(s): 0 
Gene Names: LciC
UniProt
Find proteins for Q75NZ1 (Chlamydomonas reinhardtii)
Explore Q75NZ1 
Go to UniProtKB:  Q75NZ1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75NZ1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.283 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.220 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.972α = 90
b = 88.004β = 90
c = 100.842γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Singapore National Research FoundationSingaporeNRF-RF2009-RF001-267

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-01-18
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references