3S28

The crystal structure of sucrose synthase-1 in complex with a breakdown product of the UDP-glucose

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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Literature

The Structure of Sucrose Synthase-1 from Arabidopsis thaliana and Its Functional Implications.

Zheng, Y., Anderson, S., Zhang, Y., Garavito, R.M.

(2011) J Biol Chem 286: 36108-36118

  • DOI: https://doi.org/10.1074/jbc.M111.275974
  • Primary Citation of Related Structures:  
    3S27, 3S28, 3S29

  • PubMed Abstract: 

    Sucrose transport is the central system for the allocation of carbon resources in vascular plants. During growth and development, plants control carbon distribution by coordinating sites of sucrose synthesis and cleavage in different plant organs and different cellular locations. Sucrose synthase, which reversibly catalyzes sucrose synthesis and cleavage, provides a direct and reversible means to regulate sucrose flux. Depending on the metabolic environment, sucrose synthase alters its cellular location to participate in cellulose, callose, and starch biosynthesis through its interactions with membranes, organelles, and cytoskeletal actin. The x-ray crystal structure of sucrose synthase isoform 1 from Arabidopsis thaliana (AtSus1) has been determined as a complex with UDP-glucose and as a complex with UDP and fructose, at 2.8- and 2.85-Å resolutions, respectively. The AtSus1 structure provides insights into sucrose catalysis and cleavage, as well as the regulation of sucrose synthase and its interactions with cellular targets.

    • Organizational Affiliation: 

    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sucrose synthase 1
A, B, C, D, E
A, B, C, D, E, F, G, H
816Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g20830, SUS1, T1M15.230
EC: 2.4.1.13
UniProt
Find proteins for P49040 (Arabidopsis thaliana)
Explore P49040 
Go to UniProtKB:  P49040
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49040
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP
Query on UDP
Download Ideal Coordinates CCD File 
EB [auth G]
GA [auth D]
I [auth A]
MB [auth H]
OA [auth E]
EB [auth G],
GA [auth D],
I [auth A],
MB [auth H],
OA [auth E],
Q [auth B],
WA [auth F],
Y [auth C]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
NHF
Query on NHF
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CA [auth C]
DB [auth F]
K [auth A]
LA [auth D]
LB [auth G]
CA [auth C],
DB [auth F],
K [auth A],
LA [auth D],
LB [auth G],
T [auth B],
TB [auth H],
UA [auth E]
1,5-anhydro-D-fructose
C6 H10 O5
OCLOLUFOLJIQDC-HSUXUTPPSA-N
LCN
Query on LCN
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FB [auth G]
HA [auth D]
J [auth A]
NB [auth H]
PA [auth E]
FB [auth G],
HA [auth D],
J [auth A],
NB [auth H],
PA [auth E],
R [auth B],
XA [auth F],
Z [auth C]
1,5-anhydro-D-arabino-hex-1-enitol
C6 H10 O5
CXKKSSKKIOZUNR-HSUXUTPPSA-N
MLA
Query on MLA
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BB [auth F]
EA [auth C]
JB [auth G]
MA [auth D]
O [auth A]
BB [auth F],
EA [auth C],
JB [auth G],
MA [auth D],
O [auth A],
RB [auth H],
TA [auth E],
W [auth B]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
SO4
Query on SO4
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AA [auth C]
AB [auth F]
BA [auth C]
DA [auth C]
GB [auth G]
AA [auth C],
AB [auth F],
BA [auth C],
DA [auth C],
GB [auth G],
HB [auth G],
IA [auth D],
IB [auth G],
JA [auth D],
KA [auth D],
L [auth A],
M [auth A],
N [auth A],
OB [auth H],
PB [auth H],
QA [auth E],
QB [auth H],
RA [auth E],
S [auth B],
SA [auth E],
U [auth B],
V [auth B],
YA [auth F],
ZA [auth F]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
K
Query on K
Download Ideal Coordinates CCD File 
CB [auth F]
FA [auth C]
KB [auth G]
NA [auth D]
P [auth A]
CB [auth F],
FA [auth C],
KB [auth G],
NA [auth D],
P [auth A],
SB [auth H],
VA [auth E],
X [auth B]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 276.75α = 90
b = 261.88β = 108.7
c = 160.19γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-24
    Type: Initial release
  • Version 1.1: 2011-10-26
    Changes: Database references
  • Version 1.2: 2015-04-29
    Changes: Non-polymer description
  • Version 2.0: 2020-04-22
    Changes: Atomic model, Database references
  • Version 2.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations
  • Version 2.2: 2023-09-13
    Changes: Data collection, Database references, Refinement description