3S27 | pdb_00003s27

The crystal structure of sucrose synthase-1 from Arabidopsis thaliana and its functional implications.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 
    0.237 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

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 Biological Chem 286: 36108-36118

  • DOI: https://doi.org/10.1074/jbc.M111.275974
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 766.81 kDa 
  • Atom Count: 51,283 
  • Modeled Residue Count: 6,276 
  • Deposited Residue Count: 6,528 
  • Unique protein chains: 1

Macromolecules

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|  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 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UDP

Query on UDP


Download:Ideal Coordinates CCD File
DA [auth D]
FB [auth H]
I [auth A]
KA [auth E]
P [auth B]
DA [auth D],
FB [auth H],
I [auth A],
KA [auth E],
P [auth B],
RA [auth F],
W [auth C],
YA [auth G]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
FRU

Query on FRU


Download:Ideal Coordinates CCD File
EA [auth D]
GB [auth H]
J [auth A]
LA [auth E]
Q [auth B]
EA [auth D],
GB [auth H],
J [auth A],
LA [auth E],
Q [auth B],
SA [auth F],
X [auth C],
ZA [auth G]
beta-D-fructofuranose
C6 H12 O6
RFSUNEUAIZKAJO-ARQDHWQXSA-N
MLA

Query on MLA


Download:Ideal Coordinates CCD File
BA [auth C]
DB [auth G]
IA [auth D]
KB [auth H]
N [auth A]
BA [auth C],
DB [auth G],
IA [auth D],
KB [auth H],
N [auth A],
PA [auth E],
U [auth B],
WA [auth F]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth G]
BB [auth G]
CB [auth G]
FA [auth D]
AA [auth C],
AB [auth G],
BB [auth G],
CB [auth G],
FA [auth D],
GA [auth D],
HA [auth D],
HB [auth H],
IB [auth H],
JB [auth H],
K [auth A],
L [auth A],
M [auth A],
MA [auth E],
NA [auth E],
OA [auth E],
R [auth B],
S [auth B],
T [auth B],
TA [auth F],
UA [auth F],
VA [auth F],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
K

Query on K


Download:Ideal Coordinates CCD File
CA [auth C]
EB [auth G]
JA [auth D]
LB [auth H]
O [auth A]
CA [auth C],
EB [auth G],
JA [auth D],
LB [auth H],
O [auth A],
QA [auth E],
V [auth B],
XA [auth F]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free:  0.237 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 276.212α = 90
b = 263.704β = 108.8
c = 159.663γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

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 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2024-11-27
    Changes: Data collection, Database references, Structure summary