3S28

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

PDB DOI: https://doi.org/10.2210/pdb3S28/pdb

Classification: TRANSFERASE
Organism(s): Arabidopsis thaliana
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-05-16 Released: 2011-08-24
Deposition Author(s): Zheng, Y., Garavito, R.M.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 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 Biol Chem 286: 36108-36118

PubMed: 21865170 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 762.71 kDa
Atom Count: 51,124
Modelled Residue Count: 6,246
Deposited Residue Count: 6,528
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sucrose synthase 1	A, B, C, D, E A, B, C, D, E, F, G, H	816	Arabidopsis thaliana	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49040
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UDP Query on UDP Download Ideal Coordinates CCD File SDF format, chain GA [auth D] SDF format, chain OA [auth E] SDF format, chain Q [auth B] SDF format, chain WA [auth F] SDF format, chain Y [auth C] SDF format, chain EB [auth G] SDF format, chain I [auth A] SDF format, chain MB [auth H] MOL2 format, chain GA [auth D] MOL2 format, chain OA [auth E] MOL2 format, chain Q [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain MB [auth H]	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		Interactions Focus chain EB [auth G] Focus chain GA [auth D] Focus chain I [auth A] Focus chain MB [auth H] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain WA [auth F] Focus chain Y [auth C] Interactions & Density Focus chain EB [auth G] Focus chain GA [auth D] Focus chain I [auth A] Focus chain MB [auth H] Focus chain OA [auth E] Focus chain Q [auth B] Focus chain WA [auth F] Focus chain Y [auth C]
NHF Query on NHF Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain LA [auth D] SDF format, chain LB [auth G] SDF format, chain T [auth B] SDF format, chain TB [auth H] SDF format, chain DB [auth F] SDF format, chain K [auth A] SDF format, chain UA [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth G] MOL2 format, chain T [auth B] MOL2 format, chain TB [auth H] MOL2 format, chain DB [auth F] MOL2 format, chain K [auth A] MOL2 format, chain UA [auth E]	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		Interactions Focus chain CA [auth C] Focus chain DB [auth F] Focus chain K [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain T [auth B] Focus chain TB [auth H] Focus chain UA [auth E] Interactions & Density Focus chain CA [auth C] Focus chain DB [auth F] Focus chain K [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain T [auth B] Focus chain TB [auth H] Focus chain UA [auth E]
LCN Query on LCN Download Ideal Coordinates CCD File SDF format, chain FB [auth G] SDF format, chain J [auth A] SDF format, chain NB [auth H] SDF format, chain PA [auth E] SDF format, chain Z [auth C] SDF format, chain HA [auth D] SDF format, chain R [auth B] SDF format, chain XA [auth F] MOL2 format, chain FB [auth G] MOL2 format, chain J [auth A] MOL2 format, chain NB [auth H] MOL2 format, chain PA [auth E] MOL2 format, chain Z [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain XA [auth F]	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		Interactions Focus chain FB [auth G] Focus chain HA [auth D] Focus chain J [auth A] Focus chain NB [auth H] Focus chain PA [auth E] Focus chain R [auth B] Focus chain XA [auth F] Focus chain Z [auth C] Interactions & Density Focus chain FB [auth G] Focus chain HA [auth D] Focus chain J [auth A] Focus chain NB [auth H] Focus chain PA [auth E] Focus chain R [auth B] Focus chain XA [auth F] Focus chain Z [auth C]
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain JB [auth G] SDF format, chain MA [auth D] SDF format, chain O [auth A] SDF format, chain RB [auth H] SDF format, chain TA [auth E] SDF format, chain W [auth B] SDF format, chain BB [auth F] MOL2 format, chain EA [auth C] MOL2 format, chain JB [auth G] MOL2 format, chain MA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain RB [auth H] MOL2 format, chain TA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain BB [auth F]	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		Interactions Focus chain BB [auth F] Focus chain EA [auth C] Focus chain JB [auth G] Focus chain MA [auth D] Focus chain O [auth A] Focus chain RB [auth H] Focus chain TA [auth E] Focus chain W [auth B] Interactions & Density Focus chain BB [auth F] Focus chain EA [auth C] Focus chain JB [auth G] Focus chain MA [auth D] Focus chain O [auth A] Focus chain RB [auth H] Focus chain TA [auth E] Focus chain W [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain DA [auth C] SDF format, chain GB [auth G] SDF format, chain HB [auth G] SDF format, chain IA [auth D] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain OB [auth H] SDF format, chain QB [auth H] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain IB [auth G] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain PB [auth H] SDF format, chain QA [auth E] SDF format, chain SA [auth E] SDF format, chain V [auth B] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain HB [auth G] MOL2 format, chain IA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain OB [auth H] MOL2 format, chain QB [auth H] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain IB [auth G] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain PB [auth H] MOL2 format, chain QA [auth E] MOL2 format, chain SA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F]	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		Interactions Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain DA [auth C] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain OB [auth H] Focus chain PB [auth H] Focus chain QA [auth E] Focus chain QB [auth H] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth F] Focus chain BA [auth C] Focus chain DA [auth C] Focus chain GB [auth G] Focus chain HB [auth G] Focus chain IA [auth D] Focus chain IB [auth G] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain OB [auth H] Focus chain PB [auth H] Focus chain QA [auth E] Focus chain QB [auth H] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth E] Focus chain U [auth B] Focus chain V [auth B] Focus chain YA [auth F] Focus chain ZA [auth F]
K Query on K Download Ideal Coordinates CCD File SDF format, chain CB [auth F] SDF format, chain FA [auth C] SDF format, chain KB [auth G] SDF format, chain P [auth A] SDF format, chain SB [auth H] SDF format, chain VA [auth E] SDF format, chain NA [auth D] SDF format, chain X [auth B] MOL2 format, chain CB [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain KB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain SB [auth H] MOL2 format, chain VA [auth E] MOL2 format, chain NA [auth D] MOL2 format, chain X [auth B]	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		Interactions Focus chain CB [auth F] Focus chain FA [auth C] Focus chain KB [auth G] Focus chain NA [auth D] Focus chain P [auth A] Focus chain SB [auth H] Focus chain VA [auth E] Focus chain X [auth B] Interactions & Density Focus chain CB [auth F] Focus chain FA [auth C] Focus chain KB [auth G] Focus chain NA [auth D] Focus chain P [auth A] Focus chain SB [auth H] Focus chain VA [auth E] Focus chain X [auth B]

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 = 276.75	α = 90
b = 261.88	β = 108.7
c = 160.19	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Zheng, Y.

Garavito, R.M.

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