PDBsum entry: 1d1q

Hydrolase

PDB-id: 1d1q

Biological unit* = asymmetric unit, as shown
(*as deduced by PQS)

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Protein chains

159 a.a. *

Ligands

4NP

PO4

GOL

Waters ×368

* Residue conservation analysis

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PDB id:

1d1q

Name:

Hydrolase

Title:

Crystal structure of a yeast low molecular weight protein tyrosine phosphatase (ltp1) complexed with the substrate pnpp

Structure:

Tyrosine phosphatase chain: a, b. Engineered: yes. Mutation: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: P40347 (PPAL_YEAST)

Seq:

161 a.a.

Struc:

159 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme class 1:

E.C.3.1.3.2   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

A phosphate monoester + H₂O = an alcohol + phosphate (see diagram below)

Enzyme class 2:

E.C.3.1.3.48   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Protein tyrosine phosphate + H₂O = protein tyrosine + phosphate (see diagram below)

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.

Resolution:

1.70Å

R-factor:

0.170

R-free:

0.215

Authors:

S.Wang,L.Tabernero,M.Zhang,E.Harms,R.L.Van Etten, C.V.Staufacher

Key ref:

S.Wang et al. (2000). Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate.. Biochemistry, 39, 1903-1914. [PubMed id: 10684639] [DOI: 10.1021/bi991348d]

Date:

20-Sep-99

Release date:

08-Mar-00

Related entries:

1d1p
structure of wild-type ltp1 complexed with hepes

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Key reference

DOI no: 10.1021/bi991348d

Biochemistry 39:1903-1914 (2000)

PubMed id: 10684639

Crystal structures of a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae and its complex with the substrate p-nitrophenyl phosphate.

S.Wang, L.Tabernero, M.Zhang, E.Harms, R.L.Van Etten, C.V.Stauffacher.

ABSTRACT

Low-molecular weight protein tyrosine phosphatases are virtually ubiquitous, which implies that they have important cellular functions. We present here the 2.2 A resolution X-ray crystallographic structure of wild-type LTP1, a low-molecular weight protein tyrosine phosphatase from Saccharomyces cerevisiae. We also present the structure of an inactive mutant substrate complex of LTP1 with p-nitrophenyl phosphate (pNPP) at a resolution of 1.7 A. The crystal structures of the wild-type protein and of the inactive mutant both have two molecules per asymmetric unit. The wild-type protein crystal was grown in HEPES buffer, a sulfonate anion that resembles the phosphate substrate, and a HEPES molecule was found with nearly full occupancy in the active site. Although the fold of LTP1 resembles that of its bovine counterpart BPTP, there are significant changes around the active site that explain differences in their kinetic behavior. In the crystal of the inactive mutant of LTP1, one molecule has a pNPP in the active site, while the other has a phosphate ion. The aromatic residues lining the walls of the active site cavity exhibit large relative movements between the two molecules. The phosphate groups present in the structures of the mutant protein bind more deeply in the active site (that is, closer to the position of nucleophilic cysteine side chain) than does the sulfonate group of the HEPES molecule in the wild-type structure. This further confirms the important role of the phosphate-binding loop in stabilizing the deep binding position of the phosphate group, thus helping to bring the phosphate close to the thiolate anion of nucleophilic cysteine, and facilitating the formation of the phosphoenzyme intermediate.