3T94

Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) II complexed with 5'-deoxy-5'-methylthioadenosine and sulfate

PDB DOI: https://doi.org/10.2210/pdb3T94/pdb

Classification: TRANSFERASE
Organism(s): Saccharolobus solfataricus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-02 Released: 2011-08-24
Deposition Author(s): Zhang, Y., Ealick, S.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.185
R-Value Work: 0.169
R-Value Observed: 0.170

Starting Model: experimental
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Literature

A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II.

Zhang, Y., Zwart, P.H., Ealick, S.E.

(2012) Acta Crystallogr D Biol Crystallogr 68: 249-252

PubMed: 22349226 Search on PubMed
DOI: https://doi.org/10.1107/S0907444911051699
Primary Citation of Related Structures:
3T94

PubMed Abstract:
5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) catalyzes the phosphorolytic cleavage of 5'-deoxy-5'-methylthioadenosine (MTA), a byproduct of polyamine biosynthesis. The Sulfolobus sulfataricus genome encodes two MTAPs. SsMTAP I has broad substrate specifity, accepting guanosine, inosine, adenosine and MTA, while SsMTAP II is specific for MTA. SsMTAP I forms a donut-shaped hexamer, while SsMTAP II is a hexamer formed from trimers packed face to face. The structure of SsMTAP II was originally determined in space group P1 (PDB entry 2a8y) and showed R32 pseudosymmetry. Post-analysis using phenix.xtriage showed that the correct space group is C2. Here, the structure refined in space group C2 is reported and the factors that initially led to the incorrect space-group assignment are discussed.

Organizational Affiliation

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

Macromolecule Content

Total Structure Weight: 183.91 kDa
Atom Count: 14,787
Modelled Residue Count: 1,620
Deposited Residue Count: 1,620
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-methylthioadenosine phosphorylase (MtaP)	A, B, C, D, E A, B, C, D, E, F	270	Saccharolobus solfataricus	Mutation(s): 0 EC: 2.4.2.28
UniProt
Find proteins for Q97W94 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W94 Go to UniProtKB: Q97W94
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q97W94
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MTA Query on MTA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain V [auth F] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain V [auth F]	G [auth A] J [auth B] N [auth C] P [auth D] S [auth E] G [auth A], J [auth B], N [auth C], P [auth D], S [auth E], V [auth F]	5'-DEOXY-5'-METHYLTHIOADENOSINE C₁₁ H₁₅ N₅ O₃ S WUUGFSXJNOTRMR-IOSLPCCCSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain P [auth D] Focus chain S [auth E] Focus chain V [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain W [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F]	H [auth A] I [auth A] K [auth B] L [auth B] M [auth B] H [auth A], I [auth A], K [auth B], L [auth B], M [auth B], O [auth C], Q [auth D], R [auth D], T [auth E], U [auth E], W [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain W [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.185
R-Value Work: 0.169
R-Value Observed: 0.170
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.16	α = 90
b = 138.093	β = 92.21
c = 96.56	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-08-24

Deposition Author(s):

Zhang, Y.

Ealick, S.E.

Revision History (Full details and data files)

Version 1.0: 2011-08-24
Type: Initial release
Version 1.1: 2012-02-29
Changes: Database references
Version 1.2: 2012-03-28
Changes: Database references
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

3T94

Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) II complexed with 5'-deoxy-5'-methylthioadenosine and sulfate

A corrected space group for Sulfolobus sulfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)