Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase.


Abstract

The first crystal structure of an inorganic pyrophosphatase (S-PPase) from an archaebacterium, the thermophile Sulfolobus acidocaldarius, has been solved by molecular replacement and refined to an R-factor of 19.7% at 2.7 A. S-PPase is a D3 homohexameric protein with one Mg2+ per active site in a position similar to, but not identical with, the first activating metal in mesophilic pyrophosphatases (PPase). In mesophilic PPases, Asp65, Asp70, and Asp102 coordinate the Mg2+, while only Asp65 and Asp102 do in S-PPase, and the Mg2+ moves by 0.7 A. S-PPase may therefore be deactivated at low temperature by mispositioning a key metal ion. The monomer S-PPase structure is very similar to that of Thermus thermophilus (T-PPase) and Escherichia coli (E-PPase), root-mean-square deviations around 1 A/Calpha. But the hexamer structures of S- and T-PPase are more tightly packed and more similar to each other than they are to that of E-PPase, as shown by the increase in surface area buried upon oligomerization. In T-PPase, Arg116 creates an interlocking ionic network to both twofold and threefold related monomers; S-PPase has hydrophilic interactions to threefold related monomers absent in both E- and T-PPase. In addition, the thermostable PPases have about 7% more hydrogen bonds per monomer than E-PPase, and, especially in S-PPase, additional ionic interactions anchor the C-terminus to the rest of the protein. Thermostability in PPases is thus due to subtle improvements in both monomer and oligomer interactions. Study holds ProTherm entries: 6730, 6731, 6732, 6733, 6734, 6735, 6736, 6737 Extra Details: additive : EDTA(5 mM),

Submission Details

ID: tQTdsAz94

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:32 p.m.

Version: 1

Publication Details
Leppänen VM;Nummelin H;Hansen T;Lahti R;Schäfer G;Goldman A,Protein Sci. (1999) Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase. PMID:10386872
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
2AU7 2006-08-29 1.05 The R43Q active site variant of E.coli inorganic pyrophosphatase
1I40 2001-12-05 1.1 STRUCTURE OF INORGANIC PYROPHOSPHATASE
1I6T 2001-12-05 1.2 STRUCTURE OF INORGANIC PYROPHOSPHATASE
2AU6 2006-08-29 1.2 Crystal structure of catalytic intermediate of inorganic pyrophosphatase
2AUU 2006-08-29 1.22 Inorganic pyrophosphatase complexed with magnesium pyrophosphate and fluoride
2AU9 2006-08-29 1.3 Inorganic pyrophosphatase complexed with substrate
2AU8 2006-08-29 1.65 Catalytic intermediate structure of inorganic pyrophosphatase
1OBW 1997-09-04 1.9 STRUCTURE OF INORGANIC PYROPHOSPHATASE
1MJW 1997-12-03 1.95 STRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D42N
2PRD 1995-10-28 2.0 CRYSTAL STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM THERMUS THERMOPHILUS
1MJY 1997-12-03 2.1 STRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D70N
1MJX 1997-12-03 2.15 STRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D65N
1FAJ 1996-11-08 2.15 INORGANIC PYROPHOSPHATASE
1MJZ 1997-12-03 2.2 STRUCTURE OF INORGANIC PYROPHOSPHATASE MUTANT D97N
2EIP 1996-11-08 2.2 INORGANIC PYROPHOSPHATASE
1INO 1996-04-03 2.2 RECOMBINANT INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI
1JFD 1997-12-03 2.2 STRUCTURE OF INORGANIC PYROPHOSPHATASE
1IGP 1994-12-20 2.2 X-RAY CRYSTALLOGRAPHIC STUDIES OF RECOMBINANT INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI
1IPW 1997-08-20 2.3 INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI WITH THREE MAGNESIUM IONS
4UM4 2014-11-26 2.65 STRUCTURE OF INORGANIC PYROPHOSPHATASE FROM ESCHERICHIA COLI IN COMPLEX WITH SULFATE
1QEZ 1999-04-14 2.7 SULFOLOBUS ACIDOCALDARIUS INORGANIC PYROPHOSPHATASE: AN ARCHAEL PYROPHOSPHATASE.

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
91.4 Inorganic pyrophosphatase Q8ZB98 IPYR_YERPE
94.3 Inorganic pyrophosphatase P65748 IPYR_SALTY
94.3 Inorganic pyrophosphatase P65749 IPYR_SALTI
98.9 Inorganic pyrophosphatase Q8FAG0 IPYR_ECOL6
100.0 Inorganic pyrophosphatase P0A7A9 IPYR_ECOLI
100.0 Inorganic pyrophosphatase P0A7B0 IPYR_ECO57
100.0 Inorganic pyrophosphatase P50308 IPYR_SULAC
100.0 Inorganic pyrophosphatase P38576 IPYR_THET8