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(-) Description

Title :  CHROMO DOMAIN OF HUMAN HISTONE-LYSINE N-METHYLTRANSFERASE SUV39H1
 
Authors :  R. Lam, Z. Li, J. Wang, L. Crombet, J. R. Walker, H. Ouyang, C. Bountra, J. C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. Min, Structural Gen Consortium (Sgc)
Date :  30 Apr 10  (Deposition) - 30 Jun 10  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Histone Methyltransferase, Histone-Lysine N-Methyltransferase, Suv39H1, Histone H3, Tri-Methylation, Epigenetics, Transcriptional Repression, Transcription Regulation, Chromatin, Chromo Domain, Pre- Set Domain, Set Domain, Post-Set Domain, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Wang, C. Xu, Y. Liu, K. Fan, Z. Li, X. Sun, H. Ouyang, X. Zhang, J. Zhang Y. Li, F. Mackenzie, J. Min, X. Tu
Crystal Structure Of The Human Suv39H1 Chromodomain And Its Recognition Of Histone H3K9Me2/3.
Plos One V. 7 52977 2012
PubMed-ID: 23285239  |  Reference-DOI: 10.1371/JOURNAL.PONE.0052977

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SUV39H1
    Chains: A, B, C
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21-(DE3)-V2R-PRARE2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CHROMO DOMAIN (UNP RESIDUES 44:106)
    Gene: KMT1A, SUV39H, SUV39H1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 1, SU(VAR)3-9 HOMOLOG 1, POSITION-EFFECT VARIEGATION 3-9 HOMOLOG, HISTONE H3-K9 METHYLTRANSFERASE 1, LYSINE N-METHYLTRANSFERASE 1A

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3MTS)

(-) Sites  (0, 0)

(no "Site" information available for 3MTS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MTS)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:54 -Arg A:55

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MTS)

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.SUV91_HUMAN43-91
 
 		  3A:44-91
B:44-91
C:44-91
2CHROMO_1PS00598 Chromo domain signature.SUV91_HUMAN60-80
 
 		  3A:60-80
B:60-80
C:60-80
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.SUV91_HUMAN43-91
 
 		  1A:44-91
-
-
2CHROMO_1PS00598 Chromo domain signature.SUV91_HUMAN60-80
 
 		  1A:60-80
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.SUV91_HUMAN43-91
 
 		  1-
B:44-91
-
2CHROMO_1PS00598 Chromo domain signature.SUV91_HUMAN60-80
 
 		  1-
B:60-80
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.SUV91_HUMAN43-91
 
 		  1-
-
C:44-91
2CHROMO_1PS00598 Chromo domain signature.SUV91_HUMAN60-80
 
 		  1-
-
C:60-80

(-) Exons   (0, 0)

(no "Exon" information available for 3MTS)

(-) Sequences/Alignments

Asymmetric 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:62
 aligned with SUV91_HUMAN | O43463 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:71
                                    43        53        63        73        83        93       103 
          SUV91_HUMAN    34 GISKRNLYDFEVEYLCDYKKIREQEYYLVKWRGYPDSESTWEPRQNLKCVRILKQFHKDLERELLRRHHRS 104
               SCOP domains d         3mtsa_ A: automated matches                                   SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---------.eeeeeeeee....eeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CHROMO_2  PDB: A:44-91 UniProt: 43-91            ------------- PROSITE (1)
                PROSITE (2) --------------------------CHROMO_1  PDB: A:60-8------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------- Transcript
                 3mts A  43 G---------EVEYLCDYKKIREQEYYLVKWRGYPDSESTWEPRQNLKCVRILKQFHKDLERELLRRHHRS 104
                            |        -|       53        63        73        83        93       103 
                            |        44                                                            
                           43                                                                      


Chain B from PDB  Type:PROTEIN  Length:61
 aligned with SUV91_HUMAN | O43463 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:70
                                    43        53        63        73        83        93       103
          SUV91_HUMAN    34 GISKRNLYDFEVEYLCDYKKIREQEYYLVKWRGYPDSESTWEPRQNLKCVRILKQFHKDLERELLRRHHR 103
               SCOP domains d         3mtsb_ B: automated matches                                  SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---------.eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CHROMO_2  PDB: B:44-91 UniProt: 43-91            ------------ PROSITE (1)
                PROSITE (2) --------------------------CHROMO_1  PDB: B:60-8----------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------- Transcript
                 3mts B  43 G---------EVEYLCDYKKIREQEYYLVKWRGYPDSESTWEPRQNLKCVRILKQFHKDLERELLRRHHR 103
                            |        -|       53        63        73        83        93       103
                           43        44                                                           


Chain C from PDB  Type:PROTEIN  Length:58
 aligned with SUV91_HUMAN | O43463 from UniProtKB/Swiss-Prot  Length:412

    Alignment length:67
                                    43        53        63        73        83        93       
          SUV91_HUMAN    34 GISKRNLYDFEVEYLCDYKKIREQEYYLVKWRGYPDSESTWEPRQNLKCVRILKQFHKDLERELLRR 100
               SCOP domains d         3mtsc_ C: automated matches                               SCOP domains
               CATH domains ------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Chromo-3mtsC01 C:44-92                           -------- Pfam domains (1)
           Pfam domains (2) ----------Chromo-3mtsC02 C:44-92                           -------- Pfam domains (2)
           Pfam domains (3) ----------Chromo-3mtsC03 C:44-92                           -------- Pfam domains (3)
         Sec.struct. author .---------.eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------CHROMO_2  PDB: C:44-91 UniProt: 43-91            --------- PROSITE (1)
                PROSITE (2) --------------------------CHROMO_1  PDB: C:60-8-------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------- Transcript
                 3mts C  43 G---------EVEYLCDYKKIREQEYYLVKWRGYPDSESTWEPRQNLKCVRILKQFHKDLERELLRR 100
                            |        -|       53        63        73        83        93       
                           43        44
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MTS)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Tudor (88)

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SUV91_HUMAN | O43463)
molecular function
    GO:0008757    S-adenosylmethionine-dependent methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
    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:0042054    histone methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue.
    GO:0046974    histone methyltransferase activity (H3-K9 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 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: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:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0000976    transcription regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0036123    histone H3-K9 dimethylation    The modification of histone H3 by addition of two methyl groups to lysine at position 9 of the histone.
    GO:0036124    histone H3-K9 trimethylation    The modification of histone H3 by addition of three methyl groups to lysine at position 9 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0042754    negative regulation of circadian rhythm    Any process that stops, prevents, or reduces the frequency, rate or extent of a circadian rhythm behavior.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005677    chromatin silencing complex    Any protein complex that mediates changes in chromatin structure that result in transcriptional silencing.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0000792    heterochromatin    A compact and highly condensed form of chromatin.
    GO:0005652    nuclear lamina    The fibrous, electron-dense layer lying on the nucleoplasmic side of the inner membrane of a cell nucleus, composed of lamin filaments. The polypeptides of the lamina are thought to be concerned in the dissolution of the nuclear envelope and its re-formation during mitosis. The lamina is composed of lamin A and lamin C filaments cross-linked into an orthogonal lattice, which is attached via lamin B to the inner nuclear membrane through interactions with a lamin B receptor, an IFAP, in the membrane.
    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.
    GO:0033553    rDNA heterochromatin    A region of heterochromatin located at the rDNA repeats in a chromosome.

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