PDBsum entry 1t6d

Hydrolase

PDB id

1t6d

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Contents

			Protein chains

					303 a.a. *

			Ligands

					TRS

			Metals

					_CL ×2

			Waters ×334

* Residue conservation analysis

PDB id:

1t6d

Links

Name:

Hydrolase

Title:

Miras phasing of the aquifex aeolicus ppx/gppa phosphatase: crystal structure of the type ii variant

Structure:

Exopolyphosphatase. Chain: a, b. Synonym: ppx/gppa phosphatase. Engineered: yes. Mutation: yes

Source:

Aquifex aeolicus. Organism_taxid: 224324. Strain: vf5. Gene: ppx. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.15Å

R-factor:

0.206

R-free:

0.255

Authors:

O.Kristensen,M.Laurberg,A.Liljas,J.S.Kastrup,M.Gajhede

Key ref:

O.Kristensen et al. (2004). Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family. Biochemistry, 43, 8894-8900. PubMed id: 15248747 DOI: 10.1021/bi049083c

Date:

06-May-04

Release date:

03-Aug-04

PROCHECK

	Headers

	References

Protein chains

O67040 (O67040_AQUAE) - Exopolyphosphatase from Aquifex aeolicus (strain VF5)

Seq: Struc:					312 a.a. 303 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 4 residue positions (black crosses)



		Enzyme reactions

Enzyme class 1:

E.C.3.6.1.11 - exopolyphosphatase.

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

Reaction:

[phosphate](n) + H2O = [phosphate](n-1) + phosphate + H⁺

[phosphate](n)	+	H2O	=	[phosphate](n-1)	+	phosphate	+	H(+)

Enzyme class 2:

E.C.3.6.1.40 - guanosine-5'-triphosphate,3'-diphosphate diphosphatase.

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

Reaction:

guanosine 3'-diphosphate 5'-triphosphate + H2O = guanosine 3',5'-bis(diphosphate) + phosphate + H⁺

guanosine 3'-diphosphate 5'-triphosphate	+	H2O	=	guanosine 3',5'-bis(diphosphate)	+	phosphate	+	H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1021/bi049083c	Biochemistry 43:8894-8900 (2004)
PubMed id: 15248747

Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family.
O.Kristensen, M.Laurberg, A.Liljas, J.S.Kastrup, M.Gajhede.

ABSTRACT

Exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes play central roles in the bacterial stringent response induced by starvation. The high-resolution crystal structure of the putative Aquifex aeolicus PPX/GPPA phosphatase from the actin-like ATPase domain superfamily has been determined, providing the first insights to features of the common catalytic core of the PPX/GPPA family. The protein has a two-domain structure with an active site located in the interdomain cleft. Two crystal forms were investigated (type I and II) at resolutions of 1.53 and 2.15 A, respectively. This revealed a structural flexibility that has previously been described as a "butterfly-like" cleft opening around the active site in other actin-like superfamily proteins. A calcium ion is observed at the center of this region in type I crystals, substantiating that PPX/GPPA enzymes use metal ions for catalysis. Structural analysis suggests that nucleotides bind at a similar position to that seen in other members of the superfamily.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21484095

A.F.Knowles (2011).
The GDA1_CD39 superfamily: NTPDases with diverse functions.

Purinergic Signal, 7, 21-45.

20159467

J.P.Vivian, P.Riedmaier, H.Ge, J.Le Nours, F.M.Sansom, M.C.Wilce, E.Byres, M.Dias, J.W.Schmidberger, P.J.Cowan, A.J.d'Apice, E.L.Hartland, J.Rossjohn, and T.Beddoe (2010).
Crystal structure of a Legionella pneumophila ecto -triphosphate diphosphohydrolase, a structural and functional homolog of the eukaryotic NTPDases.

Structure, 18, 228-238.

PDB codes:

3aap 3aaq 3aar

19344251

N.N.Rao, M.R.Gómez-García, and A.Kornberg (2009).
Inorganic polyphosphate: essential for growth and survival.

Annu Rev Biochem, 78, 605-647.

18458329

M.Zebisch, and N.Sträter (2008).
Structural insight into signal conversion and inactivation by NTPDase2 in purinergic signaling.

Proc Natl Acad Sci U S A, 105, 6882-6887.

PDB codes:

3cj1 3cj7 3cj9 3cja

17827150

J.Fang, F.A.Ruiz, M.Docampo, S.Luo, J.C.Rodrigues, L.S.Motta, P.Rohloff, and R.Docampo (2007).
Overexpression of a Zn2+-sensitive soluble exopolyphosphatase from Trypanosoma cruzi depletes polyphosphate and affects osmoregulation.

J Biol Chem, 282, 32501-32510.

17215253

M.Tammenkoski, V.M.Moiseev, M.Lahti, E.Ugochukwu, T.H.Brondijk, S.A.White, R.Lahti, and A.A.Baykov (2007).
Kinetic and mutational analyses of the major cytosolic exopolyphosphatase from Saccharomyces cerevisiae.

J Biol Chem, 282, 9302-9311.

16905100

J.Alvarado, A.Ghosh, T.Janovitz, A.Jauregui, M.S.Hasson, and D.A.Sanders (2006).
Origin of exopolyphosphatase processivity: Fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog.

Structure, 14, 1263-1272.

PDB code:

1u6z

17710224

T.L.Kirley, P.A.Crawford, and T.M.Smith (2006).
The structure of the nucleoside triphosphate diphosphohydrolases (NTPDases) as revealed by mutagenic and computational modeling analyses.

Purinergic Signal, 2, 379-389.

16771627

Z.Liu, and R.A.Butow (2006).
Mitochondrial retrograde signaling.

Annu Rev Genet, 40, 159-185.

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.