1YGZ | pdb_00001ygz

Crystal Structure of Inorganic Pyrophosphatase from Helicobacter pylori

PDB DOI: https://doi.org/10.2210/pdb1YGZ/pdb

Classification: HYDROLASE
Organism(s): Helicobacter pylori 26695
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2005-01-06 Released: 2005-11-01
Deposition Author(s): Wu, C.A., Lokanath, N.K., Kim, D.Y., Park, H.J., Hwang, H.Y., Kim, S.T., Suh, S.W., Kim, K.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.265 (Depositor), 0.263 (DCC)
R-Value Work:
0.206 (Depositor), 0.204 (DCC)

wwPDB Validation 3D Report Full Report

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

Literature

Structure of inorganic pyrophosphatase from Helicobacter pylori.

Wu, C.A., Lokanath, N.K., Kim, D.Y., Park, H.J., Hwang, H.Y., Kim, S.T., Suh, S.W., Kim, K.K.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1459-1464

PubMed: 16239722 Search on PubMed
DOI: https://doi.org/10.1107/S0907444905025667
Primary Citation Related Structures:
1YGZ

PubMed Abstract:
Inorganic pyrophosphatase (PPase) is a ubiquitous cytosolic enzyme which catalyzes the hydrolysis of inorganic pyrophosphate (PPi) to orthophosphate (Pi). The crystal structure of inorganic pyrophosphatase from Helicobacter pylori (H-PPase) has been solved by MAD and refined to an R factor of 20.6% at 2.6 A resolution. The crystallographic asymmetric unit contains a homohexameric H-PPase arranged as a dimer of trimers. While most of the structural elements of PPases are highly conserved in H-PPase, some unique structural features are localized in the flexible loops near the active site, suggesting that the structural flexibility of these loops is required for the catalytic efficiency of PPase.

Organizational Affiliation

Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, South Korea.

Macromolecule Content

Total Structure Weight: 116.91 kDa
Atom Count: 8,552
Modeled Residue Count: 1,032
Deposited Residue Count: 1,038
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B, C, D, E A, B, C, D, E, F	173	Helicobacter pylori 26695	Mutation(s): 4 EC: 3.6.1.1
UniProt
Find proteins for P56153 (Helicobacter pylori (strain ATCC 700392 / 26695)) Explore P56153 Go to UniProtKB: P56153
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P56153
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.265 (Depositor), 0.263 (DCC)
R-Value Work: 0.206 (Depositor), 0.204 (DCC)

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.055	α = 90
b = 115.055	β = 90
c = 73.782	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-11-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-11-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Source and taxonomy, Version format compliance
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary