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Co-crystal Structure of human SMYD3 with a MEKK2 peptide at 2.13A

Source organism: Homo sapiens
Biochemical function: histone H3K4 trimethyltransferase activity
Biological process: cellular response to dexamethasone stimulus
Cellular component: cytosol

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EC 2.1.1.354: [Histone H3]-lysine(4) N-trimethyltransferase

Reaction catalysed:
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Systematic name:
S-adenosyl-L-methionine:[histone H3]-L-lysine(4) N(6)-methyltransferase

EC 2.7.11.25: Mitogen-activated protein kinase kinase kinase

Reaction catalysed:
ATP + a protein = ADP + a phosphoprotein
Systematic name:
ATP:protein phosphotransferase (MAPKKKK-activated)
Alternative Name(s):
  • CMos
  • CRaf
  • MAP kinase kinase kinase
  • MAP3K
  • MAPKKK
  • MEK kinase
  • MEKK
  • MEKK1
  • MEKK2
  • MEKK3
  • MLK-like mitogen-activated protein triple kinase
  • MLTK
  • MLTKa
  • MLTKb
  • Mil/Raf
  • REKS
  • STK28

GO terms

Sequence families

Pfam Protein families (Pfam)
PF01753
Domain description: MYND finger
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
The deposited structure of PDB entry 5hq8 contains 2 copies of Pfam domain PF01753 (MYND finger) in Histone-lysine N-methyltransferase SMYD3. Showing 1 copy in chain A.

PF00856
Domain description: SET domain
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
The deposited structure of PDB entry 5hq8 contains 2 copies of Pfam domain PF00856 (SET domain) in Histone-lysine N-methyltransferase SMYD3. Showing 1 copy in chain A.

InterPro InterPro annotations
IPR001214
Domain description: SET domain
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
IPR046341
Domain description: SET domain superfamily
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
IPR011990
Domain description: Tetratricopeptide-like helical domain superfamily
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
IPR002893
Domain description: Zinc finger, MYND-type
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
IPR044420
Domain description: SMYD3, SET domain
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
IPR025805
Domain description: Histone-lysine N-methyltransferase SMYD3
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3

Structure domains

CATH CATH domains
2.170.270.10
Class: Mainly Beta
Architecture: Beta Complex
Topology: Beta-clip-like
Homology: SET domain
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
The deposited structure of PDB entry 5hq8 contains 2 copies of CATH domain 2.170.270.10 (Beta-clip-like) in Histone-lysine N-methyltransferase SMYD3. Showing 1 copy in chain A.
1.25.40.10
Class: Mainly Alpha
Architecture: Alpha Horseshoe
Topology: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homology: Tetratricopeptide repeat domain
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
The deposited structure of PDB entry 5hq8 contains 2 copies of CATH domain 1.25.40.10 (Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat) in Histone-lysine N-methyltransferase SMYD3. Showing 1 copy in chain A.
1.25.40.970
Class: Mainly Alpha
Architecture: Alpha Horseshoe
Topology: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homology: Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
The deposited structure of PDB entry 5hq8 contains 2 copies of CATH domain 1.25.40.970 (Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat) in Histone-lysine N-methyltransferase SMYD3. Showing 1 copy in chain A.
1.10.220.160
Class: Mainly Alpha
Architecture: Orthogonal Bundle
Topology: Annexin V; domain 1
Homology: Annexin V; domain 1
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
The deposited structure of PDB entry 5hq8 contains 2 copies of CATH domain 1.10.220.160 (Annexin V; domain 1) in Histone-lysine N-methyltransferase SMYD3. Showing 1 copy in chain A.
6.10.140.2220
Class: Special
Architecture: Helix non-globular
Topology: Helix Hairpins
Homology: Helix Hairpins
Occurring in:
  1. Histone-lysine N-methyltransferase SMYD3
The deposited structure of PDB entry 5hq8 contains 2 copies of CATH domain 6.10.140.2220 (Helix Hairpins) in Histone-lysine N-methyltransferase SMYD3. Showing 1 copy in chain A.

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