PDBsum entry 4brh

Hydrolase

PDB id

4brh

Loading ...

Contents

			Protein chains

					361 a.a.

			Ligands

					TMV ×2


					MES ×2


					DVT ×2


					GOL

			Metals

					_CL ×2


					_MG ×2

			Waters ×436

PDB id:

4brh

Links

Name:

Hydrolase

Title:

Legionella pneumophila ntpdase1 crystal form ii (closed) in complex with mg and thiamine phosphovanadate

Structure:

Ectonucleoside triphosphate diphosphohydrolase i. Chain: a, b. Fragment: residues 35-393. Synonym: ntpdase1. Engineered: yes

Source:

Legionella pneumophila. Organism_taxid: 446. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.69Å

R-factor:

0.160

R-free:

0.192

Authors:

M.Zebisch,P.Schaefer,P.Lauble,N.Straeter

Key ref:

M.Zebisch et al. (2013). Crystallographic snapshots along the reaction pathway of nucleoside triphosphate diphosphohydrolases. Structure, 21, 1460-1475. PubMed id: 23830739 DOI: 10.1016/j.str.2013.05.016

Date:

04-Jun-13

Release date:

17-Jul-13

PROCHECK

	Headers

	References

Protein chains

Q5ZUA2 (Q5ZUA2_LEGPH) - Ectonucleoside triphosphate diphosphohydrolase I from Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513)

Seq: Struc:					393 a.a. 361 a.a.*

Key:

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 3 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.3.6.1.5 - apyrase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

a ribonucleoside 5'-triphosphate + 2 H2O = a ribonucleoside 5'-phosphate + 2 phosphate + 2 H⁺

ribonucleoside 5'-triphosphate	+	2 × H2O	=	ribonucleoside 5'-phosphate	+	2 × phosphate	+	2 × H(+)

Cofactor:

Ca(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1016/j.str.2013.05.016	Structure 21:1460-1475 (2013)
PubMed id: 23830739

Crystallographic snapshots along the reaction pathway of nucleoside triphosphate diphosphohydrolases.
M.Zebisch, M.Krauss, P.Schäfer, P.Lauble, N.Sträter.

ABSTRACT

In vertebrates, membrane-bound ecto-nucleoside triphosphate diphosphohydrolases (NTPDases) on the cell surface are responsible for signal conversion and termination in purinergic signaling by extracellular nucleotides. Here we present apo and complex structures of the rat NTPDase2 extracellular domain and Legionella pneumophila NTPDase1, including a high-resolution structure with a transition-state analog. Comparison of ATP and ADP binding modes shows how NTPDases engage the same catalytic site for hydrolysis of nucleoside triphosphates and diphosphates. We find that this dual specificity is achieved at the expense of base specificity. Structural and mutational studies indicate that a conserved active-site water is replaced by the phosphate product immediately after phosphoryl transfer. Partial base specificity for purines in LpNTPDase1 is based on a different intersubunit base binding site for pyrimidine bases. A comparison of the bacterial enzyme in six independent crystal forms shows that NTPDases can undergo a domain closure motion of at least 17°.