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Asym./Biol. Unit (Jmol Viewer)

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Title :   BINARY COMPLEX OF THE MIXED LINEAGE LEUKAEMIA (MLL1) SET DOMAIN WITH THE COFACTOR PRODUCT S-ADENOSYLHOMOCYSTEINE.

Authors :   S. M. Southall, P. S. Wong, Z. Odho, S. M. Roe, J. R. Wilson

Date :   15 Dec 08 (Deposition) - 10 Feb 09 (Release) - 10 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Transcription Regulation, Chromosomal Rearrangement, Protein Lysine Methyltransferase, Proto-Oncogene, Phosphoprotein, Ubl Conjugation, S-Adenosyl-L-Methionine, Mixed Lineage Leukaemia, Polymorphism, Transcription, Metal-Binding, Zinc-Finger, Dna-Binding, Bromodomain, Transferase, Methyltransferase, Chromatin Regulator, Alternative Splicing, Histone Modification, Mll1, Zinc, Kmt2A, Nucleus, Apoptosis, Set Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. M. Southall, P. S. Wong, Z. Odho, S. M. Roe, J. R. Wilson
Structural Basis For The Requirement Of Additional Factors For Mll1 Set Domain Activity And Recognition Of Epigenetic Marks.
Mol. Cell V. 33 181 2009
PubMed-ID: 19187761 | Reference-DOI: 10.1016/J.MOLCEL.2008.12.029

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE HRX
	Chains	:	A
	EC Number	:	2.1.1.43
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTHREE-E
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	ROSETTA 2
	Fragment	:	METHYLTRANSFERASE DOMAIN, RESIDUES 3785-3969
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ZINC FINGER PROTEIN HRX, ALL-1, TRITHORAX-LIKE PROTEIN, LYSINE N-METHYLTRANSFERASE 2A, CXXC-TYPE ZINC FINGER PROTEIN 7, MLL-1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	SAH	1	Ligand/Ion	S-ADENOSYL-L-HOMOCYSTEINE
2	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:3909 , CYS A:3957 , CYS A:3959 , CYS A:3964	BINDING SITE FOR RESIDUE ZN A4970
2	AC2	SOFTWARE	HOH A:2130 , ILE A:3838 , HIS A:3839 , GLY A:3840 , ARG A:3841 , TYR A:3883 , ARG A:3903 , PHE A:3904 , ASN A:3906 , HIS A:3907 , TYR A:3944 , PRO A:3956 , ASN A:3958	BINDING SITE FOR RESIDUE SAH A4971

(no "SS Bond" information available for 2W5Y)

(no "Cis Peptide Bond" information available for 2W5Y)

(no "SAP(SNP)/Variant" information available for 2W5Y)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SET	PS50280	SET domain profile.	KMT2A_HUMAN	3829-3945	1	A:3829-3945
2	POST_SET	PS50868	Post-SET domain profile.	KMT2A_HUMAN	3953-3969	1	A:3954-3969

(no "Exon" information available for 2W5Y)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:170
 aligned with KMT2A_HUMAN | Q03164 from UniProtKB/Swiss-Prot  Length:3969

    Alignment length:177
                                  3802      3812      3822      3832      3842      3852      3862      3872      3882      3892      3902      3912      3922      3932      3942      3952      3962       
         KMT2A_HUMAN   3793 PNDEEEEEVQLKSARRATSMDLPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKFPIEDASNKLPCNCGAKKCRKFLN 3969
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.......hhhhh..hhhhhhhhhhhhhhhheeeee.....eeeee........eeee...eeee..hhhhhhhhhhhhh....eee....eeee.....hhhhhhee.....eeeeeeee..eeeeeeee........eeee....-------................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------SET  PDB: A:3829-3945 UniProt: 3829-3945                                                                             -------POST_SET          PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2w5y A 3793 PNDEEEEEVQLKSARRATSMDLPMPMRFRHLKKTSKEAVGVYRSPIHGRGLFCKRNIDAGEMVIEYAGNVIRSIQTDKREKYYDSKGIGCYMFRIDDSEVVDATMHGNAARFINHSCEPNCYSRVINIDGQKHIVIFAMRKIYRGEELTYDYKF-------KLPCNCGAKKCRKFLN 3969
                                  3802      3812      3822      3832      3842      3852      3862      3872      3882      3892      3902      3912      3922      3932      3942   |     - |    3962       
                                                                                                                                                                                  3946    3954

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2W5Y)

(no "CATH Domain" information available for 2W5Y)

(no "Pfam Domain" information available for 2W5Y)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (KMT2A_HUMAN | Q03164)

molecular function
	GO:0003680	AT DNA binding	Interacting selectively and non-covalently with oligo(A) and oligo(T) tracts of DNA (AT DNA).
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003682	chromatin binding	Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
	GO:0001046	core promoter sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is part of a core promoter region composed of the transcription start site and binding sites for the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon.
	GO:0042800	histone methyltransferase activity (H3-K4 specific)	Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 protein.
	GO:0018024	histone-lysine N-methyltransferase activity	Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0070577	lysine-acetylated histone binding	Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008168	methyltransferase activity	Catalysis of the transfer of a methyl group to an acceptor molecule.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0044212	transcription regulatory region DNA binding	Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0045322	unmethylated CpG binding	Interacting selectively and non-covalently with unmethylated CpG motifs. Unmethylated CpG dinucleotides are often associated with gene promoters.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006306	DNA methylation	The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
	GO:0009952	anterior/posterior pattern specification	The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0032922	circadian regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
	GO:0050890	cognition	The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
	GO:0060216	definitive hemopoiesis	A second wave of blood cell production that, in vertebrates, generates long-term hemopoietic stem cells that continously provide erythroid, myeloid and lymphoid lineages throughout adulthood.
	GO:0035162	embryonic hemopoiesis	The stages of blood cell formation that take place within the embryo.
	GO:0035640	exploration behavior	The specific behavior of an organism in response to a novel environment or stimulus.
	GO:0044648	histone H3-K4 dimethylation	The modification of histone H3 by addition of two methyl groups to lysine at position 4 of the histone.
	GO:0051568	histone H3-K4 methylation	The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
	GO:0080182	histone H3-K4 trimethylation	The modification of histone H3 by addition of three methyl groups to lysine at position 4 of the histone.
	GO:0043984	histone H4-K16 acetylation	The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
	GO:0048873	homeostasis of number of cells within a tissue	Any biological process involved in the maintenance of the steady-state number of cells within a population of cells in a tissue.
	GO:0051899	membrane depolarization	The process in which membrane potential decreases with respect to its steady-state potential, usually from negative potential to a more positive potential. For example, the initial depolarization during the rising phase of an action potential is in the direction from the negative steady-state resting potential towards the positive membrane potential that will be the peak of the action potential.
	GO:0032259	methylation	The process in which a methyl group is covalently attached to a molecule.
	GO:0008285	negative regulation of cell proliferation	Any process that stops, prevents or reduces the rate or extent of cell proliferation.
	GO:0018026	peptidyl-lysine monomethylation	The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
	GO:2001040	positive regulation of cellular response to drug	Any process that activates or increases the frequency, rate or extent of cellular response to drug.
	GO:0051571	positive regulation of histone H3-K4 methylation	Any process that activates or increases the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0032411	positive regulation of transporter activity	Any process that activates or increases the activity of a transporter.
	GO:0009791	post-embryonic development	The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
	GO:0006461	protein complex assembly	The aggregation, arrangement and bonding together of a set of components to form a protein complex.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0071440	regulation of histone H3-K14 acetylation	Any process that modulates the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone.
	GO:1901674	regulation of histone H3-K27 acetylation	Any process that modulates the frequency, rate or extent of histone H3-K27 acetylation.
	GO:0051569	regulation of histone H3-K4 methylation	Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 4 of histone H3.
	GO:2000615	regulation of histone H3-K9 acetylation	Any process that modulates the frequency, rate or extent of histone H3-K9 acetylation.
	GO:0048172	regulation of short-term neuronal synaptic plasticity	A process that modulates short-term neuronal synaptic plasticity, the ability of neuronal synapses to change in the short-term as circumstances require. Short-term neuronal synaptic plasticity generally involves increasing or decreasing synaptic sensitivity.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0009416	response to light stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
	GO:0035864	response to potassium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a potassium ion stimulus.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0048536	spleen development	The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
	GO:0006366	transcription from RNA polymerase II promoter	The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0008542	visual learning	Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
	GO:0071339	MLL1 complex	A protein complex that can methylate lysine-4 of histone H3. MLL1/MLL is the catalytic methyltransferase subunit, and the complex also contains the core components ASH2L, HCFC1/HCF1 WDR5 and RBBP5.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0035097	histone methyltransferase complex	A multimeric complex that is able to catalyze the addition of methyl groups to histone proteins.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	2w5y
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2agh	STRUCTURAL BASIS FOR COOPERATIVE TRANSCRIPTION FACTORBINDING TO THE CBP COACTIVATOR
2j2s	SOLUTION STRUCTURE OF THE NONMETHYL-CPG- BINDING CXXC DOMAIN OF THE LEUKAEMIA- ASSOCIATED MLL HISTONE METHYLTRANSFERASE
2w5z	TERNARY COMPLEX OF THE MIXED LINEAGE LEUKAEMIA (MLL1) SET DOMAIN WITH THE COFACTOR PRODUCT S-ADENOSYLHOMOCYSTEINE AND HISTONE PEPTIDE.

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