1S4P | pdb_00001s4p

Crystal structure of yeast alpha1,2-mannosyltransferase Kre2p/Mnt1p: ternary complex with GDP/Mn and methyl-alpha-mannoside acceptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.256 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history

Literature

Structure of Kre2p/Mnt1p: A YEAST {alpha}1,2-MANNOSYLTRANSFERASE INVOLVED IN MANNOPROTEIN BIOSYNTHESIS

Lobsanov, Y.D.Romero, P.A.Sleno, B.Yu, B.Yip, P.Herscovics, A.Howell, P.L.

(2004) J Biological Chem 279: 17921-17931

  • DOI: https://doi.org/10.1074/jbc.M312720200
  • Primary Citation Related Structures: 
    1S4N, 1S4O, 1S4P

  • PubMed Abstract: 

    Kre2p/Mnt1p is a Golgi alpha1,2-mannosyltransferase involved in the biosynthesis of Saccharomyces cerevisiae cell wall glycoproteins. The protein belongs to glycosyltransferase family 15, a member of which has been implicated in virulence of Candida albicans. We present the 2.0 A crystal structures of the catalytic domain of Kre2p/Mnt1p and its binary and ternary complexes with GDP/Mn(2+) and GDP/Mn(2+)/acceptor methyl-alpha-mannoside. The protein has a mixed alpha/beta fold similar to the glycosyltransferase-A (GT-A) fold. Although the GDP-mannose donor was used in the crystallization experiments and the GDP moiety is bound tightly to the active site, the mannose is not visible in the electron density. The manganese is coordinated by a modified DXD motif (EPD), with only the first glutamate involved in a direct interaction. The position of the donor mannose was modeled using the binary and ternary complexes of other GT-A enzymes. The C1" of the modeled donor mannose is within hydrogen-bonding distance of both the hydroxyl of Tyr(220) and the O2 of the acceptor mannose. The O2 of the acceptor mannose is also within hydrogen bond distance of the hydroxyl of Tyr(220). The structures, modeling, site-directed mutagenesis, and kinetic analysis suggest two possible catalytic mechanisms. Either a double-displacement mechanism with the hydroxyl of Tyr(220) as the potential nucleophile or alternatively, an S(N)i-like mechanism with Tyr(220) positioning the substrates for catalysis. The importance of Tyr(220) in both mechanisms is highlighted by a 3000-fold reduction in k(cat) in the Y220F mutant.


  • Organizational Affiliation
    • Program in Structural Biology and Biochemistry, Research Institute, The Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.

Macromolecule Content 

  • Total Structure Weight: 86.52 kDa 
  • Atom Count: 6,766 
  • Modeled Residue Count: 670 
  • Deposited Residue Count: 696 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glycolipid 2-alpha-mannosyltransferase
A, B
348Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: KRE2MNT1YDR483WD8035.26
EC: 2.4.1.131 (PDB Primary Data), 2.4.1 (UniProt)
UniProt
Find proteins for P27809 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P27809 
Go to UniProtKB:  P27809
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27809
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P27809-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C
8N-Glycosylation
Glycosylation Resources
GlyTouCan: G80966KZ
GlyCosmos: G80966KZ
GlyGen: G80966KZ
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
I [auth A],
O [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
J [auth A],
P [auth B]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
MMA

Query on MMA



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B]
methyl alpha-D-mannopyranoside
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
F [auth A],
L [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
M [auth B],
N [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.256 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.694α = 90
b = 101.068β = 98.81
c = 62.036γ = 90
Software Package:
Software NamePurpose
CNSrefinement
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 2.1: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-10-16
    Changes: Structure summary