7LL3: S-adenosylmethionine synthase

Name: PDB 7LL3: S-adenosylmethionine synthetase co-crystallized with UppNHp
Published: 2021-03-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

S-adenosylmethionine synthetase co-crystallized with UppNHp. Determined by X-ray diffraction at 2.24 Å resolution. Released 31 Mar 2021.

Method: X-ray diffraction
Resolution: 2.24 Å
Organism: Escherichia coli 908573
Chains: 2
Atoms: 6,069
Mol. weight: 85.35 kDa
Ligands: MG, PPK, UNP
Released: 31 Mar 2021

Explore 7LL3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7LL3 contains 30 α-helices and 36 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: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
α-helix	15-31	17
β-strand	38-46	9	2
β-strand	49-57	9	2
α-helix	64-75	12
β-strand	78-79	2	3
α-helix	80-82	3
β-strand	84-85	2	3
β-strand	90-96	7	2
α-helix	111-113	3
α-helix	114-115	2
β-strand	116	1	4
β-strand	120-127	8	5
α-helix	136-153	18
β-strand	160-173	14	1
β-strand	176-189	14	1
α-helix	195-202	8
α-helix	203-207	5
α-helix	213-215	3
β-strand	221-224	4	1
β-strand	240-241	2	2
β-strand	265	1	2
α-helix	270-287	18
β-strand	291	1	6
β-strand	293-300	8	5
β-strand	302	1	4
β-strand	309-313	5	5
β-strand	318	1	6
α-helix	322-332	11
α-helix	337-344	8
α-helix	352-355	4
α-helix	366-368	3
α-helix	373-378	6

Chain B: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-10	5	7
α-helix	15-33	19
β-strand	38-46	9	8
β-strand	49-57	9	8
α-helix	64-75	12
β-strand	78-79	2	9
α-helix	80-82	3
β-strand	84-85	2	9
β-strand	90-96	7	8
α-helix	98-99	2
α-helix	111-113	3
α-helix	114-115	2
β-strand	116	1	10
β-strand	120-127	8	11
α-helix	136-146	11
α-helix	147-151	5
β-strand	164-172	9	7
β-strand	177-187	11	7
α-helix	195-204	10
β-strand	216-224	9	7
β-strand	240-241	2	8
α-helix	246-249	4
β-strand	265	1	8
α-helix	270-287	18
β-strand	291	1	12
β-strand	293-300	8	11
β-strand	302	1	10
β-strand	309-313	5	11
β-strand	318	1	12
α-helix	322-332	11
α-helix	337-344	8
α-helix	366-368	3
α-helix	373-380	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-adenosylmethionine synthase	A, B	protein	384	Escherichia coli 908573	P0A817 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>7LL3_1 S-adenosylmethionine synthase (chains A, B)
MAKHLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTS
AWVDIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVDRADPLEQGAGDQ
GLMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDGKIVG
IDAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGPMGDC
GLTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCEIQVS
YAIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHPIYKETAAYGH
FGREHFPWEKTDKAQLLRDAAGLK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
PPK	(diphosphono)aminophosphonic acid	H6 N O9 P3	2
UNP	5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonoamino)phosphoryl]oxy}phosphoryl]uridine	C9 H16 N3 O14 P3	1

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

Primary citation

Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. Gade, M., Tan, L.L., Damry, A.M. et al. JACS Au (2021) 1:2349-2360. DOI 10.1021/jacsau.1c00464 · PubMed

Other PDB entries of the same protein (UniProt P0A817 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7R2W 1.6 Å, Mutant S-adenosylmethionine synthetase from E.coli complexed with AMPPNP and methionine
7LO2 1.89 Å, S-adenosylmethionine synthetase cocrystallized with CTP
7LOO 1.95 Å, S-adenosyl methionine transferase cocrystallized with ATP
7LOZ 2.25 Å, S-adenosylmethionine synthetase
7LOW 2.39 Å, S-adenosylmethionine synthetase
1P7L 2.5 Å, S-Adenosylmethionine synthetase complexed with AMPPNP and Met.
1RG9 2.5 Å, S-Adenosylmethionine synthetase complexed with SAM and PPNP
7LNN 2.5 Å, E. coli S-adenosyl methionine transferase co-crystallized with…
1MXA 2.8 Å, S-adenosylmethionine synthetase with ppi
1MXB 2.8 Å, S-adenosylmethionine synthetase with ADP
8BB1 2.8 Å, T3 SAM lyase in complex with S-adenosylmethionine synthase
1MXC 3.0 Å, S-adenosylmethionine synthetase with 8-br-ADP

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