spacer
spacer

PDBsum entry 1qez

Go to PDB code: 
protein metals Protein-protein interface(s) links
Hydrolase PDB id
1qez
Jmol
Contents
Protein chains
(+ 0 more) 170 a.a. *
Metals
_MG ×6
Waters ×75
* Residue conservation analysis
PDB id:
1qez
Name: Hydrolase
Title: Sulfolobus acidocaldarius inorganic pyrophosphatase: an archael pyrophosphatase.
Structure: Protein (inorganic pyrophosphatase). Chain: a, b, c, d, e, f. Synonym: ppase, s-ppase. Engineered: yes
Source: Sulfolobus acidocaldarius. Organism_taxid: 2285. Atcc: dsm 639. Collection: dsm 639. Cellular_location: cytoplasm. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: german collection of microorganisms (dsm)
Biol. unit: Homo-Hexamer (from PDB file)
Resolution:
2.70Å     R-factor:   0.197     R-free:   0.239
Authors: V.-M.Leppanen,H.Nummelin,T.Hansen,R.Lahti,G.Schafer, A.Goldman
Key ref: V.M.Leppänen et al. (1999). Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase. Protein Sci, 8, 1218-1231. PubMed id: 10386872 DOI: 10.1110/ps.8.6.1218
Date:
06-Apr-99     Release date:   14-Apr-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P50308  (IPYR_SULAC) -  Inorganic pyrophosphatase
Seq:
Struc:
173 a.a.
170 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.1.1  - Inorganic diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Diphosphate + H2O = 2 phosphate
Diphosphate
+ H(2)O
= 2 × phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     phosphate-containing compound metabolic process   1 term 
  Biochemical function     hydrolase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1110/ps.8.6.1218 Protein Sci 8:1218-1231 (1999)
PubMed id: 10386872  
 
 
Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase.
V.M.Leppänen, H.Nummelin, T.Hansen, R.Lahti, G.Schäfer, A.Goldman.
 
  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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17598086 M.J.Lee, H.Huang, W.Lin, R.R.Yang, C.L.Liu, and C.Y.Huang (2007).
Activation of Helicobacter pylori inorganic pyrophosphatase and the importance of Cys16 in thermostability, enzyme activation and quaternary structure.
  Arch Microbiol, 188, 473-482.  
16988955 T.C.Chao, H.Huang, J.Y.Tsai, C.Y.Huang, and Y.J.Sun (2006).
Kinetic and structural properties of inorganic pyrophosphatase from the pathogenic bacterium Helicobacter pylori.
  Proteins, 65, 670-680.
PDB codes: 2bqx 2bqy
16239722 C.A.Wu, N.K.Lokanath, D.Y.Kim, H.J.Park, H.Y.Hwang, S.T.Kim, S.W.Suh, and K.K.Kim (2005).
Structure of inorganic pyrophosphatase from Helicobacter pylori.
  Acta Crystallogr D Biol Crystallogr, 61, 1459-1464.
PDB code: 1ygz
14695284 B.Liu, M.Bartlam, R.Gao, W.Zhou, H.Pang, Y.Liu, Y.Feng, and Z.Rao (2004).
Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii.
  Biophys J, 86, 420-427.
PDB code: 1ude
14993699 B.Liu, X.Li, R.Gao, W.Zhou, G.Xie, M.Bartlam, H.Pang, Y.Feng, and Z.Rao (2004).
Crystallization and preliminary X-ray analysis of inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Acta Crystallogr D Biol Crystallogr, 60, 577-579.  
14765110 H.Nummelin, M.C.Merckel, J.C.Leo, H.Lankinen, M.Skurnik, and A.Goldman (2004).
The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll.
  EMBO J, 23, 701-711.
PDB code: 1p9h
11080642 T.Kajander, P.C.Kahn, S.H.Passila, D.C.Cohen, L.Lehtiö, W.Adolfsen, J.Warwicker, U.Schell, and A.Goldman (2000).
Buried charged surface in proteins.
  Structure, 8, 1203-1214.
PDB code: 1f9c
  10477309 G.Schäfer, M.Engelhard, and V.Müller (1999).
Bioenergetics of the Archaea.
  Microbiol Mol Biol Rev, 63, 570-620.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.