4V3B

The structure of alpha2,3-sialyltransferase variant 1 from Pasteurella dagmatis in complex with the donor product CMP

PDB DOI: https://doi.org/10.2210/pdb4V3B/pdb

Classification: TRANSFERASE
Organism(s): Pasteurella dagmatis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-10-17 Released: 2015-04-08
Deposition Author(s): Pavkov-Keller, T., Schmoelzer, K., Czabany, T., Luley-Goedl, C., Ribitsch, D., Schwab, H., Nidetzky, B., Gruber, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.238
R-Value Work: 0.186
R-Value Observed: 0.189

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Complete Switch from Alpha2,3- to Alpha2,6-Regioselectivity in Pasteurella Dagmatis Beta-D-Galactoside Sialyltransferase by Active-Site Redesign

Schmoelzer, K., Czabany, T., Pavkov-Keller, T., Luley-Goedl, C., Ribitsch, D., Schwab, H., Gruber, K., Nidetzky, B.

(2015) Chem Commun (Camb) 51: 3083

PubMed: 25619424 Search on PubMed
DOI: https://doi.org/10.1039/c4cc09772f
Primary Citation of Related Structures:
4V2U, 4V38, 4V39, 4V3B, 4V3C

PubMed Abstract:
Structure-guided active-site redesign of a family GT-80 β-D-galactoside sialyltransferase (from Pasteurella dagmatis) to change enzyme regioselectivity from α-2,3 in the wild type to α-2,6 in a P7H-M117A double mutant is reported. Biochemical data for sialylation of lactose together with protein crystal structures demonstrate highly precise enzyme engineering.

Organizational Affiliation

Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.

Macromolecule Content

Total Structure Weight: 46.03 kDa
Atom Count: 3,512
Modelled Residue Count: 388
Deposited Residue Count: 388
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIALYLTRANSFERASE	A	388	Pasteurella dagmatis	Mutation(s): 1
UniProt
Find proteins for K9UUI6 (Pasteurella dagmatis) Explore K9UUI6 Go to UniProtKB: K9UUI6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K9UUI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C Query on C Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CYTIDINE-5'-MONOPHOSPHATE C₉ H₁₄ N₃ O₈ P IERHLVCPSMICTF-XVFCMESISA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.238
R-Value Work: 0.186
R-Value Observed: 0.189
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.555	α = 90
b = 113.555	β = 90
c = 65.74	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-04-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-04-08
Type: Initial release
Version 1.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Other, Refinement description