4OOU

Crystal structure of beta-1,4-D-mannanase from Cryptopygus antarcticus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based investigation into the functional roles of the extended loop and substrate-recognition sites in an endo-beta-1,4-d-mannanase from the Antarctic springtail, Cryptopygus antarcticus.

Kim, M.K.An, Y.J.Song, J.M.Jeong, C.S.Kang, M.H.Kwon, K.K.Lee, Y.H.Cha, S.S.

(2014) Proteins 82: 3217-3223

  • DOI: 10.1002/prot.24655
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Endo-β-1,4-D-mannanase from the Antarctic springtail, Cryptopygus antarcticus (CaMan), is a cold-adapted β-mannanase that has the lowest optimum temperature (30°C) of all known β-mannanases. Here, we report the apo- and mannopentaose (M5) complex str ...

    Endo-β-1,4-D-mannanase from the Antarctic springtail, Cryptopygus antarcticus (CaMan), is a cold-adapted β-mannanase that has the lowest optimum temperature (30°C) of all known β-mannanases. Here, we report the apo- and mannopentaose (M5) complex structures of CaMan. Structural comparison of CaMan with other β-mannanases from the multicellular animals reveals that CaMan has an extended loop that alters topography of the active site. Structural and mutational analyses suggest that this extended loop is linked to the cold-adapted enzymatic activity. From the CaMan-M5 complex structure, we defined the mannose-recognition subsites and observed unreported M5 binding site on the surface of CaMan.


    Organizational Affiliation

    Marine Biotechnology Research Division, Korea Institute of Ocean Science and Technology, Ansan, 426-744, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Beta-1,4-mannanase
B, A
388Cryptopygus antarcticusMutation(s): 0 
EC: 3.2.1.78
Find proteins for B4XC07 (Cryptopygus antarcticus)
Go to UniProtKB:  B4XC07
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download SDF File 
Download CCD File 
A, B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 74.237α = 90.00
b = 84.476β = 90.00
c = 164.057γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
REFMACrefinement
MOLREPphasing
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-06
    Type: Initial release
  • Version 1.1: 2014-11-05
    Type: Database references