ISDA

Deposition Date 2009-02-02

Release Date 2009-05-05

Last Version Date 2023-09-06

Entry Detail

PDB ID:

3G3R

Keywords:

BIOSYNTHETIC PROTEIN

Title:

Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+

Biological Source:

Source Organism:

Saccharomyces cerevisiae (Taxon ID: 4932)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.00 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Vacuolar transporter chaperone 4
Gene (Uniprot):VTC4
Chain IDs:A, B
Chain Length:295
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae

UniProt ID:P47075 Pfam ID:PF09359

[{'entity_id': ['2'], 'name': ['PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER'], 'comp_id': ['ANP'], 'asym_id': ['C', 'I'], 'ndb_seq_num': ['1'], 'pdb_seq_num': ['1000'], 'auth_seq_num': ['1000'], 'pdb_mon_id': ['ANP'], 'auth_mon_id': ['ANP'], 'pdb_strand_id': ['A', 'B'], 'pdb_ins_code': ['.']}, {'entity_id': ['3'], 'name': ['MANGANESE (II) ION'], 'comp_id': ['MN'], 'asym_id': ['D', 'J'], 'ndb_seq_num': ['1'], 'pdb_seq_num': ['1001'], 'auth_seq_num': ['1001'], 'pdb_mon_id': ['MN'], 'auth_mon_id': ['MN'], 'pdb_strand_id': ['A', 'B'], 'pdb_ins_code': ['.']}, {'entity_id': ['5'], 'name': ['SODIUM ION'], 'comp_id': ['NA'], 'asym_id': ['H'], 'ndb_seq_num': ['1'], 'pdb_seq_num': ['1'], 'auth_seq_num': ['1'], 'pdb_mon_id': ['NA'], 'auth_mon_id': ['NA'], 'pdb_strand_id': ['A'], 'pdb_ins_code': ['.']}, {'entity_id': ['4'], 'name': ['SULFATE ION'], 'comp_id': ['SO4'], 'asym_id': ['E', 'F', 'G', 'K', 'L', 'M'], 'ndb_seq_num': ['1'], 'pdb_seq_num': ['2', '5', '7', '3', '4', '6'], 'auth_seq_num': ['2', '5', '7', '3', '4', '6'], 'pdb_mon_id': ['SO4'], 'auth_mon_id': ['SO4'], 'pdb_strand_id': ['A', 'B'], 'pdb_ins_code': ['.']}]

Primary Citation

Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase.

Hothorn, M, Neumann, H, Lenherr, E.D, Wehner, M, Rybin, V, Hassa, P.O, Uttenweiler, A, Reinhardt, M, Schmidt, A, Seiler, J, Ladurner, A.G, Herrmann, C, Scheffzek, K, Mayer, A.Show

Science 324 513 516 (2009)

PMID: 19390046 DOI: 10.1126/science.1168120

Abstact

Polyphosphate (polyP) occurs ubiquitously in cells, but its functions are poorly understood and its synthesis has only been characterized in bacteria. Using x-ray crystallography, we identified a eukaryotic polyphosphate polymerase within the membrane-integral vacuolar transporter chaperone (VTC) complex. A 2.6 angstrom crystal structure of the catalytic domain grown in the presence of adenosine triphosphate (ATP) reveals polyP winding through a tunnel-shaped pocket. Nucleotide- and phosphate-bound structures suggest that the enzyme functions by metal-assisted cleavage of the ATP gamma-phosphate, which is then in-line transferred to an acceptor phosphate to form polyP chains. Mutational analysis of the transmembrane domain indicates that VTC may integrate cytoplasmic polymer synthesis with polyP membrane translocation. Identification of the polyP-synthesizing enzyme opens the way to determine the functions of polyP in lower eukaryotes.

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