3G3R: Eukaryotic polyphosphate polymerase

Crystal structure of a eukaryotic polyphosphate polymerase in complex with AppNHp-Mn2+. Determined by X-ray diffraction at 2.0 Å resolution. Released 5 May 2009.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Saccharomyces cerevisiae
Chains: 2
Atoms: 5,129
Mol. weight: 71.27 kDa
Ligands: MN, ANP
Released: 5 May 2009

Explore 3G3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3G3R contains 25 α-helices and 23 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	196-203	8	1
α-helix	208-216	9
α-helix	220	1
β-strand	221-223	3	1
α-helix	232-235	4
β-strand	236-243	8	1
α-helix	248-255	8
β-strand	261-268	8	1
β-strand	275-286	12	1
β-strand	289-300	12	1
α-helix	301-303	3
α-helix	304-308	5
α-helix	314-324	11
α-helix	329-348	20
β-strand	352-366	15	1
β-strand	369-384	16	1
α-helix	414-416	3
β-strand	417-419	3	1
β-strand	423-430	8	1
α-helix	435-438	4
α-helix	439-446	8
β-strand	451-452	2	1
α-helix	458-466	9

Chain B: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	194-203	10	2
α-helix	205-207	3
α-helix	208-215	8
α-helix	220	1
β-strand	221	1	2
β-strand	222-224	3	1
β-strand	236-243	8	2
α-helix	248-255	8
β-strand	261-268	8	2
β-strand	275-282	8	2
α-helix	286-288	3
β-strand	293-300	8	2
α-helix	301-303	3
α-helix	304-309	6
α-helix	314-317	4
α-helix	319-323	5
α-helix	329-348	20
β-strand	352-366	15	2
β-strand	369-384	16	2
α-helix	414-416	3
β-strand	417-419	3	2
β-strand	423-432	10	2
α-helix	439-445	7
β-strand	451-452	2	2
α-helix	458-466	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vacuolar transporter chaperone 4	A, B	protein	295	Saccharomyces cerevisiae	P47075 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3G3R_1 Vacuolar transporter chaperone 4 (chains A, B)
GAMGKQQNFVRQTTKYWVHPDNITELKLIILKHLPVLVFNTNKEFEREDSAITSIYFDNE
NLDLYYGRLRKDEGAEAHRLRWYGGMSTDTIFVERKTHREDWTGEKSVKARFALKERHVN
DFLKGKYTVDQVFAKMRKEGKKPMNEIENLEALASEIQYVMLKKKLRPVVRSFYNRTAFQ
LPGDARVRISLDTELTMVREDNFDGVDRTHKNWRRTDIGVDWPFKQLDDKDICRFPYAVL
EVKLQTQLGQEPPEWVRELVGSHLVEPVPKFSKFIHGVATLLNDKVDSIPFWLPQ

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Water and common crystallization additives (NA, SO4) are not listed.

Primary citation

Catalytic core of a membrane-associated eukaryotic polyphosphate polymerase. Hothorn, M., Neumann, H., Lenherr, E.D. et al. Science (2009) 324:513-516. DOI 10.1126/science.1168120 · PubMed

Other PDB entries of the same protein (UniProt P47075 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3G3T 1.85 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with orthophosphate
3G3U 2.07 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with pyrophosphate
5IIT 2.13 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…
3G3Q 2.64 Å, Crystal structure of a eukaryotic polyphosphate polymerase in complex with a phosphate…
5IIG 2.99 Å, Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase…
7YTJ 3.0 Å, Cryo-EM structure of VTC complex
5IIQ 3.03 Å, Structure of the SPX-TTM domain fragment of the yeast inorganic polyphophate polymerase…
9UMG 3.04 Å, Cryo-EM structure of VTC complex(Vtc5/Vtc4/Vtc3/Vtc1)
8I6V 3.06 Å, Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)
5LNC 3.29 Å, Structure of SPX domain of the yeast inorganic polyphophate polymerase Vtc4 crystallized…

Browse structure collections

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