5HQB

A Glycoside Hydrolase Family 97 enzyme (E480Q) in complex with Panose from Pseudoalteromonas sp. strain K8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.137 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structures of PspAG97A alpha-glucoside hydrolase reveal a novel mechanism for chloride induced activation.

He, C.Li, J.Li, W.Xue, Y.Fang, Z.Fang, W.Zhang, X.Wang, X.Xiao, Y.

(2016) J Struct Biol 196: 426-436

  • DOI: 10.1016/j.jsb.2016.09.009
  • Primary Citation of Related Structures:  
    5HQ4, 5HQA, 5HQB, 5HQC

  • PubMed Abstract: 
  • Here we report the first crystal structure of a secretory α-glucoside hydrolase isolated from Pseudoalteromonas sp. K8, PspAG97A, which belongs to glycoside hydrolase family 97 and exhibits halophilic property. PspAG97A lacks an acidic surface, that is considered essential for protein stability at high salinity ...

    Here we report the first crystal structure of a secretory α-glucoside hydrolase isolated from Pseudoalteromonas sp. K8, PspAG97A, which belongs to glycoside hydrolase family 97 and exhibits halophilic property. PspAG97A lacks an acidic surface, that is considered essential for protein stability at high salinity. Interestingly, PspAG97A unusually contains a chloride ion coordinated by the guanidinium group of Arg171 and the main chain amide groups of Tyr172 and Glu173 at the active site. The structures of PspAG97A complexed with acarbose and panose demonstrate that residues Glu173, Arg171 and Asn170 for subsite +1 decide the substrate specificity of the enzyme for the α-1,6-glucosidic linkage. Structural alterations observed in the R171K variant and enzyme kinetic experiments focusing on chloride assisted activation suggest that the active site chloride serves to properly orient Glu173, Arg171 and Asn170 to facilitate substrate recognition. Furthermore, the chloride assists the binding of Glu173 to the conserved calcium ion and plays an essential role in properly positioning the base catalyst Glu456. In sum, our results provide valuable insight into the structural basis of protein halophilicity.


    Organizational Affiliation

    School of Life Sciences, Anhui University, Hefei, Anhui 230601, China; Anhui Provincial Engineering Technology Research Center of Microorganisms and Biocatalysis, Hefei, Anhui 230601, China. Electronic address: yzxiao@ahu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Alpha-glucosidaseA669Pseudoalteromonas sp. K8Mutation(s): 1 
UniProt
Find proteins for A0A0Y0DFX2 (Pseudoalteromonas sp. K8)
Explore A0A0Y0DFX2 
Go to UniProtKB:  A0A0Y0DFX2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0Y0DFX2
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseB 3N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G05704WW
GlyCosmos:  G05704WW
GlyGen:  G05704WW
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

Download Ideal Coordinates CCD File 
M [auth A]FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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N [auth A]UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.137 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.167α = 90
b = 119.167β = 90
c = 181.832γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2016-01-21 
  • Released Date: 2017-01-11 
  • Deposition Author(s): Li, J., He, C., Xiao, Y.

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-11
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary