6KMS | pdb_00006kms

Crystal structure of human N6amt1-Trm112 in complex with SAM (space group I422)

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth C]	Methyltransf_11_2	e6kmsC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
D	Methyltransf_11_2	e6kmsD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: Methyltransf_11_2	ECOD (1.6)
B [auth A]	Trm112p	e6kmsA1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Trm112p	ECOD (1.6)
C [auth B]	Trm112p	e6kmsB1	A: few secondary structure elements	X: Trm112p-like (From Topology)	H: Trm112p-like (From Topology)	T: Trm112p-like	F: Trm112p	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C], D	PF05175	Methyltransferase small domain (MTS)	Methyltransferase small domain	This domain is found in ribosomal RNA small subunit methyltransferase C (eg Swiss:P44453) as well as other methyltransferases (eg Swiss:Q53742).	Domain
B [auth A], C [auth B]	PF03966	Trm112p-like protein (Trm112p)	Trm112p-like protein	The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA ...	The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. Trm112p is required for tRNA methylation in S. cerevisiae and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W [1]. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast [2]. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], D	Methyltransferase N6AMT1	protein-lysine N-methyltransferase activity histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H4K12 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity protein-lysine N-methyltransferase activity histone H4 methyltransferase activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity histone methyltransferase activity histone H4K12 methyltransferase activity lysine N-methyltransferase activity protein methyltransferase activity histone modifying activity N-methyltransferase activity methyltransferase activity catalytic activity protein-glutamine N-methyltransferase activity DNA-methyltransferase activity catalytic activity, acting on DNA site-specific DNA-methyltransferase (adenine-specific) activity catalytic activity, acting on a nucleic acid binding nucleic acid binding cation binding ion binding S-adenosyl-L-methionine binding sulfur compound binding small molecule binding arsenite methyltransferase activity	regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis regulation of growth regulation of biological process regulation of cellular process regulation of cellular component organization biological regulation growth positive regulation of biological process positive regulation of cell growth regulation of cell growth cell growth cellular component organization positive regulation of growth cellular process cellular component organization or biogenesis positive regulation of cellular process RNA metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic RNA biosynthetic process nucleobase-containing compound metabolic process positive regulation of metabolic process DNA-templated transcription nucleic acid biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling positive regulation of macromolecule metabolic process transcription initiation at RNA polymerase II promoter regulation of biosynthetic process epigenetic regulation of gene expression primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process DNA-templated transcription initiation regulation of gene expression biosynthetic process positive regulation of gene expression transcription initiation-coupled chromatin remodeling regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process protein methylation macromolecule methylation protein alkylation methylation macromolecule modification peptidyl-glutamine methylation protein metabolic process protein modification process cellular response to stimulus arsonoacetate metabolic process response to stimulus oxoacid metabolic process cellular response to xenobiotic stimulus carboxylic acid metabolic process organic acid metabolic process xenobiotic metabolic process response to xenobiotic stimulus cellular response to chemical stimulus response to chemical small molecule metabolic process toxin metabolic process secondary metabolic process negative regulation of biological process negative regulation of cellular process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of gene expression, epigenetic	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol eRF1 methyltransferase complex protein-containing complex catalytic complex methyltransferase complex transferase complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B [auth A], C [auth B]	Multifunctional methyltransferase subunit TRM112-like protein	enzyme regulator activity enzyme activator activity molecular function activator activity methyltransferase regulator activity molecular function regulator activity tRNA methyltransferase activator activity protein heterodimerization activity protein binding binding protein dimerization activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity enzyme regulator activity enzyme activator activity molecular function activator activity methyltransferase regulator activity molecular function regulator activity tRNA methyltransferase activator activity protein heterodimerization activity protein binding binding protein dimerization activity catalytic activity, acting on a protein transferase activity, transferring one-carbon groups protein methyltransferase activity transferase activity methyltransferase activity catalytic activity	ribonucleoprotein complex biogenesis regulation of cellular process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process positive regulation of metabolic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process ribonucleoprotein complex biogenesis regulation of cellular process positive regulation of biological process RNA metabolic process rRNA processing positive regulation of rRNA processing regulation of primary metabolic process nucleobase-containing compound metabolic process cellular component biogenesis RNA biosynthetic process positive regulation of metabolic process ribosome biogenesis nucleic acid biosynthetic process regulation of RNA metabolic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process cellular component organization or biogenesis RNA processing rRNA metabolic process positive regulation of cellular process regulation of biosynthetic process positive regulation of nucleobase-containing compound metabolic process regulation of biological process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression nucleobase-containing compound biosynthetic process regulation of rRNA processing macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process positive regulation of macromolecule biosynthetic process positive regulation of gene expression, epigenetic cellular component organization DNA-templated transcription transcription by RNA polymerase II positive regulation of biosynthetic process chromatin organization chromatin remodeling transcription initiation at RNA polymerase II promoter epigenetic regulation of gene expression DNA-templated transcription initiation positive regulation of gene expression transcription initiation-coupled chromatin remodeling tRNA processing tRNA modification macromolecule methylation tRNA metabolic process RNA modification methylation macromolecule modification RNA methylation tRNA methylation protein methylation protein alkylation peptidyl-glutamine methylation protein metabolic process protein modification process ribosomal small subunit biogenesis maturation of SSU-rRNA RNA (guanine-N7)-methylation rRNA methylation rRNA modification rRNA (guanine-N7)-methylation rRNA base methylation ribosomal large subunit biogenesis maturation of LSU-rRNA	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm protein-containing complex tRNA (m2G10) methyltransferase complex catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex membrane-bounded organelle nucleus membrane-enclosed lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol perinuclear region of cytoplasm protein-containing complex tRNA (m2G10) methyltransferase complex catalytic complex methyltransferase complex transferase complex tRNA methyltransferase complex membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], D	IPR004557	Eukaryotic/archaeal PrmC-related	Family
A [auth C], D	IPR002052	DNA methylase, N-6 adenine-specific, conserved site	Conserved Site
A [auth C], D	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
A [auth C], D	IPR007848	Methyltransferase small domain	Domain
A [auth C], D	IPR052190	Eukaryotic/Archaeal PrmC-Related Methyltransferase	Family
B [auth A], C [auth B]	IPR039127	Multifunctional methyltransferase subunit Trm112	Family
B [auth A], C [auth B]	IPR005651	Trm112-like	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C], D	Pharos: Q9Y5N5	Down syndrome lung cancer osteosarcoma
B [auth A], C [auth B]	Pharos: Q9UI30	alopecia areata diabetes mellitus leprosy ovarian cancer psoriasis vitiligo attention deficit hyperactivity disorder, inattentive type hypertensive disorder lung cancer plasma cell myeloma sclerosing cholangitis Crohn disease inflammatory bowel disease lymphoplasmacytic lymphoma primary biliary cholangitis alopecia areata diabetes mellitus leprosy ovarian cancer psoriasis vitiligo attention deficit hyperactivity disorder, inattentive type hypertensive disorder lung cancer plasma cell myeloma sclerosing cholangitis Crohn disease inflammatory bowel disease lymphoplasmacytic lymphoma primary biliary cholangitis skin basal cell carcinoma

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.