7NWO

A carbohydrate binding module family 9 (CBM9) from Caldicellulosiruptor kristjanssonii in complex with glucose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.256 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Structural and Functional Analysis of a Multimodular Hyperthermostable Xylanase-Glucuronoyl Esterase from Caldicellulosiruptor kristjansonii .

Krska, D., Mazurkewich, S., Brown, H.A., Theibich, Y., Poulsen, J.N., Morris, A.L., Koropatkin, N.M., Lo Leggio, L., Larsbrink, J.

(2021) Biochemistry 60: 2206-2220

  • DOI: 10.1021/acs.biochem.1c00305
  • Primary Citation of Related Structures:  
    7NN3, 7NWN, 7NWO, 7NWP, 7NWQ

  • PubMed Abstract: 

    • The hyperthermophilic bacterium Caldicellulosiruptor kristjansonii encodes an unusual enzyme, Ck Xyn10C-GE15A, which incorporates two catalytic domains, a xylanase and a glucuronoyl esterase, and five carbohydrate-binding modules (CBMs) from families 9 and 22 ...

    The hyperthermophilic bacterium Caldicellulosiruptor kristjansonii encodes an unusual enzyme, Ck Xyn10C-GE15A, which incorporates two catalytic domains, a xylanase and a glucuronoyl esterase, and five carbohydrate-binding modules (CBMs) from families 9 and 22. The xylanase and glucuronoyl esterase catalytic domains were recently biochemically characterized, as was the ability of the individual CBMs to bind insoluble polysaccharides. Here, we further probed the abilities of the different CBMs from Ck Xyn10C-GE15A to bind to soluble poly- and oligosaccharides using affinity gel electrophoresis, isothermal titration calorimetry, and differential scanning fluorimetry. The results revealed additional binding properties of the proteins compared to the former studies on insoluble polysaccharides. Collectively, the results show that all five CBMs have their own distinct binding preferences and appear to complement each other and the catalytic domains in targeting complex cell wall polysaccharides. Additionally, through renewed efforts, we have achieved partial structural characterization of this complex multidomain protein. We have determined the structures of the third CBM9 domain (CBM9.3) and the glucuronoyl esterase (GE15A) by X-ray crystallography. CBM9.3 is the second CBM9 structure determined to date and was shown to bind oligosaccharide ligands at the same site but in a different binding mode compared to that of the previously determined CBM9 structure from Thermotoga maritima . GE15A represents a unique intermediate between reported fungal and bacterial glucuronoyl esterase structures as it lacks two inserted loop regions typical of bacterial enzymes and a third loop has an atypical structure. We also report small-angle X-ray scattering measurements of the N-terminal CBM22.1-CBM22.2-Xyn10C construct, indicating a compact arrangement at room temperature.

    Organizational Affiliation: 

    Wallenberg Wood Science Center, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-xylanaseA [auth AAA]215Caldicellulosiruptor kristjanssonii I77R1BMutation(s): 0 
Gene Names: Calkr_2245
EC: 3.2.1.8
UniProt
Find proteins for E4S6E9 (Caldicellulosiruptor kristjanssonii (strain ATCC 700853 / DSM 12137 / I77R1B))
Explore E4S6E9 
Go to UniProtKB:  E4S6E9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE4S6E9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC
Download Ideal Coordinates CCD File 
S [auth AAA]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
BGC (Subject of Investigation/LOI)
Query on BGC
Download Ideal Coordinates CCD File 
B [auth AAA]beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N		 Ligand Interaction
PEG
Query on PEG
Download Ideal Coordinates CCD File 
C [auth AAA],
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
C [auth AAA],
D [auth AAA],
E [auth AAA],
F [auth AAA],
G [auth AAA],
H [auth AAA],
I [auth AAA],
J [auth AAA]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
Download Ideal Coordinates CCD File 
K [auth AAA],
L [auth AAA],
M [auth AAA],
N [auth AAA],
O [auth AAA]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
P [auth AAA],
Q [auth AAA],
R [auth AAA]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.256 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 172.61α = 90
b = 172.61β = 90
c = 172.61γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden2016-01065
Swedish Energy AgencySweden2016-011207
Novo Nordisk FoundationDenmarkNNF17OC0027698
Knut and Alice Wallenberg FoundationSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-07
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references