PDBsum entry 7ea8

Gene regulation

PDB id: 7ea8

Contents

Protein chains

245 a.a.

101 a.a.

78 a.a.

104 a.a.

92 a.a.

94 a.a.

DNA/RNA

Ligands

SAM

Metals

_ZN ×3

PDB id:

7ea8

Name:

Gene regulation

Title:

Human setd2 bound to a nucleosome containing oncohistone mutations

Structure:

Histone-lysine n-methyltransferase setd2. Chain: l. Synonym: hif-1,huntingtin yeast partner b,huntingtin-interacting protein 1,hip-1,huntingtin-interacting protein b,lysine n- methyltransferase 3a,protein-lysine n-methyltransferase setd2,set domain-containing protein 2,hset2,p231hbp. Engineered: yes. Histone h3.3. Chain: a, e.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: setd2, hif1, hypb, kiaa1732, kmt3a, set2, hspc069. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: h2ac7, h2afg, hist1h2ad. Gene: h2bc21, h2bfq, hist2h2be. Synthetic: yes.

Authors:

H.Jing,Y.Liu

Key ref:

Y.Liu et al. (2021). Cryo-Em structure of setd2/set2 methyltransferase bou nucleosome containing oncohistone mutations.. Cell discov, 7, 32. PubMed id: 33972509 DOI: 10.1038/S41421-021-00261-6

Date:

06-Mar-21 Release date: 14-Jul-21

Protein chain

Q9BYW2  (SETD2_HUMAN) -  Histone-lysine N-methyltransferase SETD2 from Homo sapiens

Seq: 2564 a.a.

Struc: 245 a.a.

Protein chain

Q6PI79  (H33_XENLA) -  Histone H3.3 from Xenopus laevis

Seq: 136 a.a.

Struc: 101 a.a.*

Protein chains

P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis

Seq: 103 a.a.

Struc: 78 a.a.

Protein chains

P20671  (H2A1D_HUMAN) -  Histone H2A type 1-D from Homo sapiens

Seq: 130 a.a.

Struc: 104 a.a.

Protein chains

P06899  (H2B1J_HUMAN) -  Histone H2B type 1-J from Homo sapiens

Seq: 126 a.a.

Struc: 92 a.a.

Protein chain

Q6PI79  (H33_XENLA) -  Histone H3.3 from Xenopus laevis

Seq: 136 a.a.

Struc: 94 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

C-G-A-G-A-A-T-C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T-T-G-G-T-C-G-T-A-G-A- 122 bases

T-G-C-C-T-G-G-A-G-A-C-T-A-G-G-G-A-G-T-A-A-T-C-C-C-C-T-T-G-G-C-G-G-T-T-A-A-A-A- 122 bases

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D, E, F, G, H: E.C.?
• Enzyme class 3: Chain L: E.C.2.1.1.- - ?????
• Enzyme class 4: Chain L: E.C.2.1.1.359 - [histone H3]-lysine(36) N-trimethyltransferase.
• Reaction: L-lysyl₃₆-[histone H3] + 3 S-adenosyl-L-methionine = N₆,N₆,N₆- trimethyl-L-lysyl₃₆-[histone H3] + 3 S-adenosyl-L-homocysteine + 3 H⁺

L-lysyl(36)-[histone H3] + 3 × S-adenosyl-L-methionine (Bound ligand (Het Group name = SAM) corresponds exactly) = N(6),N(6),N(6)- trimethyl-L-lysyl(36)-[histone H3] + 3 × S-adenosyl-L-homocysteine + 3 × H(+)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site