9BOX: Serine hydroxymethyltransferase, mitochondrial

Name: PDB 9BOX: Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid)
Published: 2024-08-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase (hSHMT2) with PLP-glycine external aldimine and 5-formyltetrahydrofolate (folinic acid). Determined by X-ray diffraction at 2.1 Å resolution. Released 28 Aug 2024.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 15,295
Mol. weight: 208.43 kDa
Ligands: A1AQW, FFO
Released: 28 Aug 2024

Explore 9BOX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9BOX contains 97 α-helices and 80 β-strands across 4 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: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	54-69	16
β-strand	71-72	2	1
α-helix	82-88	7
α-helix	91-94	4
β-strand	99-100	2	2
β-strand	103-104	2	2
α-helix	110-126	17
β-strand	134-137	4	3
α-helix	143-154	12
β-strand	160-164	5	3
α-helix	166-168	3
α-helix	172-174	3
β-strand	177	1	4
β-strand	182	1	4
α-helix	185-187	3
β-strand	191-195	5	3
β-strand	197-198	2	5
β-strand	203-204	2	5
α-helix	206-216	11
β-strand	220-223	4	3
α-helix	234-244	11
β-strand	247-251	5	3
α-helix	256-260	5
α-helix	267-269	3
β-strand	273-277	5	3
β-strand	288-293	6	3
β-strand	296-299	4	6
α-helix	305	1
β-strand	306-308	3	6
α-helix	309	1
α-helix	312-317	6
α-helix	318-323	6
α-helix	329-342	14
α-helix	345-367	23
β-strand	371-372	2	7
α-helix	373-375	3
β-strand	381-385	5	7
α-helix	387-389	3
α-helix	393-401	9
β-strand	405-406	2	1
β-strand	408-410	3	7
β-strand	423-427	5	7
α-helix	429-432	4
α-helix	438-461	24
α-helix	465-474	10
α-helix	476-493	18

Chain B: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	54-69	16
β-strand	71-72	2	8
α-helix	82-88	7
α-helix	91-94	4
β-strand	99-100	2	9
β-strand	103-104	2	9
α-helix	110-126	17
β-strand	134-137	4	10
α-helix	143-154	12
β-strand	160-164	5	10
α-helix	172-174	3
β-strand	177	1	11
β-strand	182	1	11
α-helix	185-187	3
β-strand	191-195	5	10
β-strand	197-198	2	12
β-strand	203-204	2	12
α-helix	206-216	11
β-strand	220-223	4	10
α-helix	234-244	11
β-strand	247-251	5	10
α-helix	256-260	5
α-helix	267-269	3
β-strand	273-277	5	10
β-strand	288-293	6	10
β-strand	296-299	4	13
β-strand	306-308	3	13
α-helix	312-317	6
α-helix	318-323	6
α-helix	329-342	14
α-helix	345-367	23
β-strand	371-372	2	14
α-helix	373-375	3
β-strand	381-385	5	14
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	8
β-strand	408-410	3	14
β-strand	423-427	5	14
α-helix	429-432	4
α-helix	438-461	24
α-helix	465-474	10
α-helix	476-494	19

Chain C: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	54-69	16
β-strand	71-72	2	15
α-helix	82-88	7
α-helix	91-94	4
β-strand	99-100	2	16
β-strand	103-104	2	16
α-helix	110-126	17
β-strand	134-137	4	17
α-helix	143-154	12
β-strand	160-164	5	17
α-helix	166-168	3
α-helix	172-174	3
β-strand	177	1	18
β-strand	182	1	18
α-helix	185-187	3
β-strand	191-195	5	17
β-strand	197	1	19
β-strand	204	1	19
α-helix	206-216	11
β-strand	220-223	4	17
α-helix	234-244	11
β-strand	247-251	5	17
α-helix	256-260	5
α-helix	267-269	3
β-strand	273-277	5	17
β-strand	288-293	6	17
α-helix	311-317	7
α-helix	318-323	6
α-helix	329-342	14
α-helix	345-367	23
β-strand	371-372	2	20
α-helix	373-375	3
β-strand	381-385	5	20
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	15
β-strand	408-410	3	20
β-strand	423-427	5	20
α-helix	429-432	4
α-helix	438-460	23
α-helix	465-474	10
α-helix	476-493	18

Chain D: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	54-69	16
β-strand	71-72	2	21
α-helix	82-88	7
α-helix	91-94	4
β-strand	99-100	2	22
β-strand	103-104	2	22
α-helix	110-126	17
β-strand	134-137	4	23
α-helix	143-154	12
β-strand	160-164	5	23
α-helix	166-168	3
α-helix	172-174	3
β-strand	177	1	24
β-strand	182	1	24
α-helix	185-187	3
β-strand	191-195	5	23
β-strand	197	1	25
β-strand	204	1	25
α-helix	206-216	11
β-strand	220-223	4	23
α-helix	234-244	11
β-strand	247-251	5	23
α-helix	256-260	5
α-helix	267-269	3
β-strand	273-277	5	23
β-strand	288-293	6	23
α-helix	312-317	6
α-helix	318-323	6
α-helix	329-342	14
α-helix	345-367	23
β-strand	371-372	2	26
α-helix	373-375	3
β-strand	381-385	5	26
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	21
β-strand	408-410	3	26
β-strand	423-427	5	26
α-helix	429-432	4
α-helix	438-461	24
α-helix	465-474	10
α-helix	476-494	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, mitochondrial	A, B, C, D	protein	462	Homo sapiens	P34897 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9BOX_1 Serine hydroxymethyltransferase, mitochondrial (chains A, B, C, D)
WTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPG
KRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIM
GLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLII
AGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTL
RGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQA
CTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLEL
VSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKT
AKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH

Ligands and cofactors

ID	Name	Formula	Copies
A1AQW	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)gly…	C10 H13 N2 O7 P	4
FFO	N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}a…	C20 H23 N7 O7	4

Primary citation

Universality of critical active site glutamate as an acid-base catalyst in serine hydroxymethyltransferase function. Drago, V.N., Phillips, R.S., Kovalevsky, A. Chem Sci (2024) 15:12827-12844. DOI 10.1039/d4sc03187c · PubMed

Other PDB entries of the same protein (UniProt P34897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8AQL 1.23 Å, High-resolution crystal structure of human SHMT2
29LK 1.26 Å, High-resolution structure of human SHMT2 in complex with PLP-Ser (external aldimine)
9RWD 1.3 Å, High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)
32JY 1.8 Å, Structure of the pathogenic variant G423S of Human SHMT2
6DK3 2.04 Å, Human mitochondrial serine hydroxymethyltransferase 2
32JA 2.2 Å, Structure of the pathogenic variant T186R of Human SHMT2 in the apo open dimeric…
6QVL 2.28 Å, Human SHMT2 in complex with pemetrexed
6M5O 2.3 Å, Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with…
6QVG 2.32 Å, Human SHMT2 in complex with lometrexol
8GKW 2.38 Å, Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine…
5V7I 2.47 Å, Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial)…
8FJT 2.47 Å, Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine…

Browse structure collections

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