1UP2 | pdb_00001up2

Structure of the endoglucanase Cel6 from Mycobacterium tuberculosis in complex with glucose-isofagomine at 1.9 angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.177 (Depositor), 0.190 (DCC) 
  • R-Value Work: 
    0.132 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.134 (Depositor) 

Starting Model: other
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Mycobacterium Tuberculosis Strains Possess Functional Cellulases.

Varrot, A.Leydier, S.Pell, G.Macdonald, J.M.Stick, R.V.Henrissat, B.Gilbert, H.J.Davies, G.J.

(2005) J Biological Chem 280: 20181

  • DOI: https://doi.org/10.1074/jbc.C500142200
  • Primary Citation Related Structures: 
    1UOZ, 1UP0, 1UP2, 1UP3

  • PubMed Abstract: 

    The genomes of various Mycobacterium tuberculosis strains encode proteins that do not appear to play a role in the growth or survival of the bacterium in its mammalian host, including some implicated in plant cell wall breakdown. Here we show that M. tuberculosis H37Rv does indeed possess a functional cellulase. The x-ray crystal structure of this enzyme, in ligand complex forms, from 1.9 to 1.1A resolution, reveals a highly conserved substrate-binding cleft, which affords similar, and unusual, distortion of the substrate at the catalytic center. The endoglucanase activity, together with the existence of a putative membrane-associated crystalline polysaccharide-binding protein, may reflect the ancestral soil origin of the Mycobacterium or hint at a previously unconsidered environmental niche.


  • Organizational Affiliation
    • York Structural Biology Laboratory, Department of Chemistry, University of York, York, Y010 5YW, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 31.8 kDa 
  • Atom Count: 2,637 
  • Modeled Residue Count: 293 
  • Deposited Residue Count: 294 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
CELA1 PROTEIN294Mycobacterium tuberculosis H37RvMutation(s): 0 
EC: 3.2.1
UniProt
Find proteins for Q79G13 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore Q79G13 
Go to UniProtKB:  Q79G13
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79G13
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PG

Query on 1PG



Download:Ideal Coordinates CCD File
J [auth A]2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
C11 H24 O6
SLNYBUIEAMRFSZ-UHFFFAOYSA-N
BGC

Query on BGC



Download:Ideal Coordinates CCD File
C [auth A],
E [auth A]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
IFM

Query on IFM



Download:Ideal Coordinates CCD File
B [auth A],
D [auth A]
5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE
C6 H13 N O3
QPYJXFZUIJOGNX-HSUXUTPPSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT

Query on ACT



Download:Ideal Coordinates CCD File
H [auth A],
I [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MHO
Query on MHO
A
L-PEPTIDE LINKINGC5 H11 N O3 SMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.177 (Depositor), 0.190 (DCC) 
  • R-Value Work:  0.132 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.134 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.788α = 90
b = 92.83β = 90
c = 46.695γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-18
    Type: Initial release
  • Version 1.1: 2015-07-15
    Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.4: 2024-10-23
    Changes: Structure summary