PDBsum entry: 1gxu

Phosphatase

PDB id: 1gxu

Contents

Protein chain

88 a.a. *

Ligands

2HP

Waters ×109

* Residue conservation analysis

PDB id:

1gxu

Name:

Phosphatase

Title:

Hydrogenase maturation protein hypf "acylphosphatase-like" n-terminal domain (hypf-acp) in complex with a substrate. Crystal grown in the presence of carbamoylphosphate

Structure:

Hydrogenase maturation protein hypf. Chain: a. Fragment: acylphosphatase-like domain, residues 1-91. Engineered: yes

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PDB file)

Resolution:

1.27Å R-factor: 0.133 R-free: 0.161

Authors:

C.Rosano,S.Zuccotti,M.Stefani,M.Bucciantini,G.Ramponi, M.Bolognesi

Key ref:

C.Rosano et al. (2002). Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain. J Mol Biol, 321, 785-796. PubMed id: 12206761 DOI: 10.1016/S0022-2836(02)00713-1

Date:

11-Apr-02 Release date: 12-Sep-02

Protein chain

P30131  (HYPF_ECOLI) -  Carbamoyltransferase hypF

Seq: 750 a.a.

Struc: 88 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 

• Biological process: protein carbamoylation (1 term)
• Biochemical function: carboxyl- or carbamoyltransferase activity (2 terms)

DOI no: 10.1016/S0022-2836(02)00713-1

J Mol Biol 321:785-796 (2002)

PubMed id: 12206761

Crystal structure and anion binding in the prokaryotic hydrogenase maturation factor HypF acylphosphatase-like domain.

C.Rosano, S.Zuccotti, M.Bucciantini, M.Stefani, G.Ramponi, M.Bolognesi.

ABSTRACT

[NiFe]-hydrogenases require a set of complementary and regulatory proteins for correct folding and maturation processes. One of the essential regulatory proteins, HypF (82kDa) contains a N-terminal acylphosphatase (ACT)-like domain, a sequence motif shared with enzymes catalyzing O-carbamoylation, and two zinc finger motifs similar to those found in the DnaJ chaperone. The HypF acylphosphatase domain is thought to support the conversion of carbamoylphosphate into CO and CN(-), promoting coordination of these ligands to the hydrogenase metal cluster. It has been shown recently that the HypF N-terminal domain can aggregate in vitro to yield fibrils matching those formed by proteins linked to amyloid diseases. The 1.27A resolution HypF acylphosphatase domain crystal structure (residues 1-91; R-factor 13.1%) shows a domain fold of betaalphabetabetaalphabeta topology, as observed in mammalian acylphosphatases specifically catalyzing the hydrolysis of the carboxyl-phosphate bonds in acylphosphates. The HypF N-terminal domain can be assigned to the ferredoxin structural superfamily, to which RNA-binding domains of small nuclear ribonucleoproteins and some metallochaperone proteins belong. Additionally, the HypF N-terminal domain displays an intriguing structural relationship to the recently discovered ACT domains. The structures of different HypF acylphosphatase domain complexes show a phosphate binding cradle comparable to the P-loop observed in unrelated phosphatase families. On the basis of the catalytic mechanism proposed for acylphosphatases, whereby residues Arg23 and Asn41 would support substrate orientation and the nucleophilic attack of a water molecule on the phosphate group, fine structural features of the HypF N-terminal domain putative active site region may account for the lack of acylphosphatase activity observed for the expressed domain. The crystallographic analyses here reported were undertaken to shed light on the molecular bases of inactivity, folding, misfolding and aggregation of the HypF N-terminal acylphosphatase domain.

Selected figure(s)

Figure 3.
Figure 3. Stereo views of overlaid C^a traces for the following protein pairs: (a) HypF-ACP and CT bovine ACP (gray and salmon colors, respectively). Residues Arg23 and Asn41 and bound anions (sulfate bound to CT bovine ACP, green; phosphate bound to HypF-ACP, purple) are also displayed. (b) HypF-ACP and Atx1 (gray and red, respectively); the phosphate moiety bound to CT bovine ACP is also displayed.

Figure 4.
Figure 4. Stereo view of the HypF-ACP putative active site region in the presence of: (a) sulfate and Cl - (green sticks and yellow sphere), and phosphate and water (W10) (purple-red sticks and blue sphere); (b) a mono view of the electrostatic charge distribution (mapped at ±3kT/e level), at the HypF-ACP putative active site region, in the absence of bound anionic ligands. The evident cavity is the anion binding site; the 19-22 polypeptide stretch forming the anion cradle is portrayed in transparence. All Figures were produced with Dino (http://www.bioz.unibas.ch/~xray/dino).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 321, 785-796) copyright 2002.

Figures were selected by an automated process.