1G8H | pdb_00001g8h

ATP SULFURYLASE FROM S. CEREVISIAE: THE TERNARY PRODUCT COMPLEX WITH APS AND PPI

PDB DOI: https://doi.org/10.2210/pdb1G8H/pdb

Classification: TRANSFERASE
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2000-11-17 Released: 2001-05-23
Deposition Author(s): Ullrich, T.C., Blaesse, M., Huber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.245 (Depositor), 0.243 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.194 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of ATP sulfurylase from Saccharomyces cerevisiae, a key enzyme in sulfate activation.

Ullrich, T.C., Blaesse, M., Huber, R.

(2001) EMBO J 20: 316-329

PubMed: 11157739 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/emboj/20.3.316
Primary Citation Related Structures:
1G8F, 1G8G, 1G8H

PubMed Abstract:
ATP sulfurylases (ATPSs) are ubiquitous enzymes that catalyse the primary step of intracellular sulfate activation: the reaction of inorganic sulfate with ATP to form adenosine-5'-phosphosulfate (APS) and pyrophosphate (PPi). With the crystal structure of ATPS from the yeast Saccharomyces cerevisiae, we have solved the first structure of a member of the ATP sulfurylase family. We have analysed the crystal structure of the native enzyme at 1.95 Angstroms resolution using multiple isomorphous replacement (MIR) and, subsequently, the ternary enzyme product complex with APS and PPi bound to the active site. The enzyme consists of six identical subunits arranged in two stacked rings in a D:3 symmetric assembly. Nucleotide binding causes significant conformational changes, which lead to a rigid body structural displacement of domains III and IV of the ATPS monomer. Despite having similar folds and active site design, examination of the active site of ATPS and comparison with known structures of related nucleotidylyl transferases reveal a novel ATP binding mode that is peculiar to ATP sulfurylases.

Organizational Affiliation

Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany. tullrich@biochem.mpg.de

Macromolecule Content

Total Structure Weight: 119.55 kDa
Atom Count: 8,917
Modeled Residue Count: 1,020
Deposited Residue Count: 1,022
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SULFATE ADENYLYLTRANSFERASE	A, B	511	Saccharomyces cerevisiae	Mutation(s): 0 EC: 2.7.7.4
UniProt
Find proteins for P08536 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08536 Go to UniProtKB: P08536
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08536
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADX Query on ADX Download:Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain RA [auth B]	RA [auth B], S [auth A]	ADENOSINE-5'-PHOSPHOSULFATE C₁₀ H₁₄ N₅ O₁₀ P S IRLPACMLTUPBCL-KQYNXXCUSA-N		Interactions Focus chain RA [auth B] Focus chain S [auth A] Interactions & Density Focus chain RA [auth B] Focus chain S [auth A]
POP Query on POP Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain SA [auth B]	SA [auth B], T [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain SA [auth B] Focus chain T [auth A] Interactions & Density Focus chain SA [auth B] Focus chain T [auth A]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain O [auth A] SDF format, chain GA [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth B] SDF format, chain E [auth A] SDF format, chain CA [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain O [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain O [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain CA [auth B] mmCIF format, chain C [auth A]	C [auth A] CA [auth B] D [auth A] DA [auth B] E [auth A] C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], O [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain O [auth A] Interactions & Density Focus chain C [auth A] Focus chain CA [auth B] Focus chain D [auth A] Focus chain DA [auth B] Focus chain E [auth A] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain O [auth A]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain UA [auth B] SDF format, chain V [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain Z [auth A] SDF format, chain ZA [auth B] SDF format, chain XA [auth B] SDF format, chain W [auth A] SDF format, chain VA [auth B] SDF format, chain U [auth A] SDF format, chain TA [auth B] SDF format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain WA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] TA [auth B] U [auth A] UA [auth B] AA [auth A], BA [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], XA [auth B], Y [auth A], YA [auth B], Z [auth A], ZA [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain XA [auth B] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain Z [auth A] Focus chain ZA [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain J [auth A] SDF format, chain HA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth B] mmCIF format, chain H [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth B]	H [auth A] HA [auth B] J [auth A] JA [auth B] K [auth A] H [auth A], HA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain HA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Interactions & Density Focus chain H [auth A] Focus chain HA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain LA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B]	L [auth A], LA [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain LA [auth B] Interactions & Density Focus chain L [auth A] Focus chain LA [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain MA [auth B] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain PA [auth B] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain IA [auth B] SDF format, chain I [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain I [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain I [auth A]	I [auth A] IA [auth B] M [auth A] MA [auth B] N [auth A] I [auth A], IA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain IA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Interactions & Density Focus chain I [auth A] Focus chain IA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.245 (Depositor), 0.243 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 186.011	α = 90
b = 186.011	β = 90
c = 223.812	γ = 120

Software Package:

Software Name	Purpose
CCP4	model building
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2001-05-23

Deposition Author(s):

Ullrich, T.C.

Blaesse, M.

Huber, R.

Revision History (Full details and data files)

Version 1.0: 2001-05-23
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description