7JWF

Crystal structure of PdGH110B D344N in complex with alpha-(1,3)-galactobiose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

The structure of a family 110 glycoside hydrolase provides insight into the hydrolysis of alpha-1,3-galactosidic linkages in lambda-carrageenan and blood group antigens.

McGuire, B.E., Hettle, A.G., Vickers, C., King, D.T., Vocadlo, D.J., Boraston, A.B.

(2020) J Biol Chem 295: 18426-18435

  • DOI: https://doi.org/10.1074/jbc.RA120.015776
  • Primary Citation of Related Structures:  
    7JW4, 7JWF

  • PubMed Abstract: 

    α-Linked galactose is a common carbohydrate motif in nature that is processed by a variety of glycoside hydrolases from different families. Terminal Galα1-3Gal motifs are found as a defining feature of different blood group and tissue antigens, as well as the building block of the marine algal galactan λ-carrageenan. The blood group B antigen and linear α-Gal epitope can be processed by glycoside hydrolases in family GH110, whereas the presence of genes encoding GH110 enzymes in polysaccharide utilization loci from marine bacteria suggests a role in processing λ-carrageenan. However, the structure-function relationships underpinning the α-1,3-galactosidase activity within family GH110 remain unknown. Here we focus on a GH110 enzyme (PdGH110B) from the carrageenolytic marine bacterium Pseudoalteromonas distincta U2A. We showed that the enzyme was active on Galα1-3Gal but not the blood group B antigen. X-ray crystal structures in complex with galactose and unhydrolyzed Galα1-3Gal revealed the parallel β-helix fold of the enzyme and the structural basis of its inverting catalytic mechanism. Moreover, an examination of the active site reveals likely adaptations that allow accommodation of fucose in blood group B active GH110 enzymes or, in the case of PdGH110, accommodation of the sulfate groups found on λ-carrageenan. Overall, this work provides insight into the first member of a predominantly marine clade of GH110 enzymes while also illuminating the structural basis of α-1,3-galactoside processing by the family as a whole.

    • Organizational Affiliation: 

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycoside hydrolase family 110
A, B, C, D
620Pseudoalteromonas distinctaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-galactopyranose-(1-3)-beta-D-galactopyranoseE [auth F],
F [auth E],
G,
H		2N/A
Glycosylation Resources
GlyTouCan:  G24432YB
GlyCosmos:  G24432YB
GlyGen:  G24432YB
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE
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PG [auth D]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PG4
Query on PG4
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AB [auth A],
OG [auth D]		TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
MLT
Query on MLT
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DD [auth C],
I [auth A],
QG [auth D],
UE [auth D]		D-MALATE
C4 H6 O5
BJEPYKJPYRNKOW-UWTATZPHSA-N
IOD
Query on IOD
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AA [auth A]
AC [auth B]
AE [auth C]
AG [auth D]
BA [auth A]
AA [auth A],
AC [auth B],
AE [auth C],
AG [auth D],
BA [auth A],
BC [auth B],
BE [auth C],
BG [auth D],
CA [auth A],
CC [auth B],
CE [auth C],
CG [auth D],
DA [auth A],
DC [auth B],
DE [auth C],
DG [auth D],
EA [auth A],
EC [auth B],
EE [auth C],
EG [auth D],
FA [auth A],
FC [auth B],
FE [auth C],
FG [auth D],
GA [auth A],
GC [auth B],
GE [auth C],
GF [auth D],
GG [auth D],
HA [auth A],
HC [auth B],
HE [auth C],
HF [auth D],
HG [auth D],
IA [auth A],
IC [auth B],
IE [auth C],
IF [auth D],
IG [auth D],
JA [auth A],
JC [auth B],
JE [auth C],
JF [auth D],
JG [auth D],
KA [auth A],
KC [auth B],
KE [auth C],
KF [auth D],
KG [auth D],
LA [auth A],
LC [auth B],
LE [auth C],
LF [auth D],
LG [auth D],
MA [auth A],
MC [auth B],
ME [auth C],
MF [auth D],
NA [auth A],
NC [auth B],
NE [auth C],
NF [auth D],
OA [auth A],
OC [auth B],
OE [auth C],
OF [auth D],
PA [auth A],
PC [auth B],
PE [auth C],
PF [auth D],
QA [auth A],
QC [auth B],
QE [auth C],
QF [auth D],
RA [auth A],
RC [auth B],
RD [auth C],
RE [auth C],
RF [auth D],
SA [auth A],
SC [auth B],
SD [auth C],
SF [auth D],
TA [auth A],
TC [auth B],
TD [auth C],
TF [auth D],
UA [auth A],
UB [auth B],
UC [auth B],
UD [auth C],
UF [auth D],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VD [auth C],
VF [auth D],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WD [auth C],
WF [auth D],
X [auth A],
XA [auth A],
XB [auth B],
XD [auth C],
XF [auth D],
Y [auth A],
YA [auth A],
YB [auth B],
YD [auth C],
YF [auth D],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZD [auth C],
ZF [auth D]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
MLA
Query on MLA
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MG [auth D]MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
MLI
Query on MLI
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NG [auth D]MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
EDO
Query on EDO
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AF [auth D]
BF [auth D]
CF [auth D]
DF [auth D]
ED [auth C]
AF [auth D],
BF [auth D],
CF [auth D],
DF [auth D],
ED [auth C],
EF [auth D],
FD [auth C],
FF [auth D],
GB [auth B],
GD [auth C],
HB [auth B],
HD [auth C],
IB [auth B],
ID [auth C],
J [auth A],
JB [auth B],
JD [auth C],
K [auth A],
KB [auth B],
KD [auth C],
L [auth A],
LB [auth B],
LD [auth C],
M [auth A],
MB [auth B],
MD [auth C],
N [auth A],
NB [auth B],
ND [auth C],
O [auth A],
OB [auth B],
OD [auth C],
P [auth A],
PB [auth B],
PD [auth C],
Q [auth A],
QB [auth B],
QD [auth C],
R [auth A],
RB [auth B],
S [auth A],
SB [auth B],
T [auth A],
TB [auth B],
U [auth A],
VE [auth D],
WE [auth D],
XE [auth D],
YE [auth D],
ZE [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT
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CB [auth A],
CD [auth C],
XC [auth B]		ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA
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BB [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL
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AD [auth B]
BD [auth B]
DB [auth A]
EB [auth A]
FB [auth A]
AD [auth B],
BD [auth B],
DB [auth A],
EB [auth A],
FB [auth A],
RG [auth D],
SE [auth C],
TE [auth C],
YC [auth B],
ZC [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.517α = 90
b = 124.763β = 93.86
c = 142.423γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2020-11-18
    Changes: Database references
  • Version 1.2: 2021-01-06
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description