2G9Y: Alkaline phosphatase

Structure of S102T E. coli alkaline phosphatase in presence of phosphate at 2.00 A resolution. Determined by X-ray diffraction at 2.0 Å resolution. Released 10 Oct 2006.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Escherichia coli
Chains: 2
Atoms: 7,188
Mol. weight: 94.91 kDa
Ligands: PO4, MG, ZN
Released: 10 Oct 2006

Explore 2G9Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2G9Y contains 40 α-helices and 59 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: 19 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	30-34	5
β-strand	44-50	7	1
α-helix	55-61	7
α-helix	62-66	5
β-strand	80-85	6	1
β-strand	88-89	2	2
β-strand	96-97	2	2
α-helix	102-111	10
β-strand	116	1	2
β-strand	120	1	3
β-strand	122	1	4
β-strand	128	1	4
α-helix	132-138	7
β-strand	142-150	9	1
α-helix	154-157	4
β-strand	163	1	3
α-helix	171-177	7
α-helix	183-185	3
α-helix	191-198	8
β-strand	202-206	5	1
α-helix	209-212	4
β-strand	214	1	5
β-strand	215	1	6
β-strand	221	1	6
β-strand	224	1	5
α-helix	225-231	7
β-strand	235-237	3	1
α-helix	240-245	6
β-strand	255-258	4	1
α-helix	264-266	3
β-strand	268-269	2	7
α-helix	271-273	3
β-strand	274-275	2	8
β-strand	284	1	8
β-strand	287-288	2	7
α-helix	299-310	12
β-strand	317-323	7	1
α-helix	325-331	7
α-helix	335-359	25
β-strand	362-367	6	1
β-strand	371	1	9
β-strand	375-377	3	8
β-strand	386-391	6	8
β-strand	397-402	6	8
β-strand	413	1	9
β-strand	417-422	6	1
α-helix	426-429	4
β-strand	431-434	4	1
α-helix	435-446	12

Chain B: 21 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	30-35	6
α-helix	41-42	2
β-strand	44-50	7	1
α-helix	55-65	11
β-strand	80-85	6	1
β-strand	88-89	2	10
β-strand	96-97	2	10
α-helix	102-111	10
β-strand	120	1	11
β-strand	122	1	12
β-strand	128	1	12
α-helix	132-138	7
β-strand	142-150	9	1
α-helix	154-157	4
β-strand	163	1	11
α-helix	171-177	7
α-helix	183-185	3
α-helix	191-198	8
β-strand	202-206	5	1
α-helix	208-212	5
β-strand	214	1	13
β-strand	215	1	14
β-strand	221	1	14
β-strand	224	1	13
α-helix	225-231	7
β-strand	235-237	3	1
α-helix	240-245	6
β-strand	255-258	4	1
α-helix	264-266	3
β-strand	268-269	2	15
α-helix	271-273	3
β-strand	274	1	16
α-helix	277-280	4
α-helix	282-283	2
β-strand	284	1	16
β-strand	287-288	2	15
α-helix	299-310	12
β-strand	317-323	7	1
α-helix	325-331	7
α-helix	335-359	25
β-strand	362-367	6	1
β-strand	371	1	17
β-strand	375-377	3	16
β-strand	386-391	6	16
β-strand	397-402	6	16
β-strand	413	1	17
β-strand	417-422	6	1
α-helix	426-429	4
β-strand	431-434	4	1
α-helix	435-446	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Alkaline phosphatase	A, B	protein	449	Escherichia coli	P00634 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2G9Y_1 Alkaline phosphatase (chains A, B)
TPEMPVLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITA
ARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDTAASATAWSTGVKTYNGAL
GVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPG
NALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDA
ASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLA
QMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEG
NTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIA
AYGPHAANVVGLTDQTDLFYTMKAALGLK

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	4

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

Primary citation

Trapping the tetrahedral intermediate in the alkaline phosphatase reaction by substitution of the active site serine with threonine. Wang, J., Kantrowitz, E.R. Protein Sci (2006) 15:2395-2401. DOI 10.1110/ps.062351506 · PubMed

Other PDB entries of the same protein (UniProt P00634 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3TG0 1.2 Å, E. coli alkaline phosphatase with bound inorganic phosphate
3BDF 1.4 Å, Crystal structure of metal-free E. coli alkaline phosphatase (T155V)
3BDG 1.4 Å, Crystal structure of wild-type/T155V mixed dimer of E. coli alkaline phosphatase
1Y6V 1.6 Å, Structure of E. coli Alkaline Phosphatase in presence of cobalt at 1.60 A resolution
1ED8 1.75 Å, Structure of E. Coli alkaline phosphatase inhibited by the inorganic phosphate at 1.75A…
1ED9 1.75 Å, Structure of E. Coli alkaline phosphatase without the inorganic phosphate at 1.75A…
1Y7A 1.77 Å, Structure of D153H/K328W E. coli alkaline phosphatase in presence of cobalt at 1.77 A…
7N6M 1.82 Å, Crystal structure of the substrate-binding domain of E. coli DnaK in complex with the…
3BDH 1.85 Å, Crystal structure of zinc-deficient wild-type E. coli alkaline phosphatase
1B8J 1.9 Å, Alkaline phosphatase complexed with vanadate
1ALK 2.0 Å, Reaction mechanism of alkaline phosphatase based on crystal structures. Two metal ion…
1EW9 2.0 Å, Alkaline phosphatase (e.c. 3.1.3.1) complex with mercaptomethyl phosphonate

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