4XSU | pdb_00004xsu

Crystal structure of Anabaena Alr3699/HepE in complex with UDP and glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 
    0.267 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structural and enzymatic analyses of a glucosyltransferase Alr3699/HepE involved in Anabaena heterocyst envelop polysaccharide biosynthesis

Wang, X.P.Jiang, Y.L.Dai, Y.N.Cheng, W.Chen, Y.Zhou, C.Z.

(2016) Glycobiology 26: 520-531

  • DOI: https://doi.org/10.1093/glycob/cwv167
  • Primary Citation Related Structures: 
    4XSO, 4XSP, 4XSR, 4XSU

  • PubMed Abstract: 

    Formation of the heterocyst envelope polysaccharide (HEP) is a key process for cyanobacterial heterocyst differentiation. The maturation of HEP in Anabaena sp. strain PCC 7120 is controlled by a gene cluster termed HEP island in addition to an operon alr3698-alr3699, which encodes two putative proteins termed Alr3698/HepD and Alr3699/HepE. Here we report the crystal structures of HepE in the apo-form and three complex forms that bind to UDP-glucose (UDPG), UDP&glucose, and UDP, respectively. The overall structure of HepE displays a typical GT-B fold of glycosyltransferases, comprising two separate β/α/β Rossmann-fold domains that form an inter-domain substrate-binding crevice. Structural analyses combined with enzymatic assays indicate that HepE is a glucosyltransferase using UDPG as a sugar donor. Further site-directed mutageneses enable us to assign the key residues that stabilize the sugar donor and putative acceptor. Based on the comparative structural analyses, we propose a putative catalytic cycle of HepE, which undergoes "open-closed-open" conformational changes upon binding to the substrates and release of products. These findings provide structural and catalytic insights into the first enzyme involved in the HEP biosynthesis pathway.


  • Organizational Affiliation
    • Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 86.87 kDa 
  • Atom Count: 5,962 
  • Modeled Residue Count: 735 
  • Deposited Residue Count: 776 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alr3699 proteinA [auth B],
B [auth A]
388Nostoc sp. PCC 7120 = FACHB-418Mutation(s): 0 
Gene Names: alr3699
EC: 2.4.1
UniProt
Find proteins for A0ACD6B985 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576))
Explore A0ACD6B985 
Go to UniProtKB:  A0ACD6B985
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0ACD6B985
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP

Query on UDP



Download:Ideal Coordinates CCD File
D [auth B],
K [auth A]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
GLC

Query on GLC



Download:Ideal Coordinates CCD File
C [auth B],
J [auth A]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth B]
F [auth B]
G [auth B]
H [auth B]
I [auth B]
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
L [auth A],
M [auth A],
N [auth A],
O [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
P [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free:  0.267 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.991α = 90
b = 130.991β = 90
c = 156.327γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling
MOLREPmodel building
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31370757

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary