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(-) Description

Title :  THE STRUCTURE OF THE SUV4-20H2 TERNARY COMPLEX WITH HISTONE H4
 
Authors :  S. M. Southall, N. B. Cronin, J. R. Wilson
Date :  14 May 12  (Deposition) - 22 May 13  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transferase, Epigenetics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Southall, N. B. Cronin, J. R. Wilson
A Novel Route To Product Specificity In The Suv4-20 Family Of Histone H4K20 Methyltransferases.
Nucleic Acids Res. V. 42 661 2014
PubMed-ID: 24049080  |  Reference-DOI: 10.1093/NAR/GKT776

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H2
    Chains: A, B
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SET DOMAIN, RESIDUES 1-246
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: SUPPRESSOR OF VARIEGATION 4-20 HOMOLOG 2, SU(VAR)4-20 HOMOLOG 2, SUV4-20H2
 
Molecule 2 - HISTONE H4 PEPTIDE
    Chains: C
    Fragment: RESIDUES 18-26
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synthetic: YES

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 21)

Asymmetric Unit (4, 21)
No.NameCountTypeFull Name
1EDO16Ligand/Ion1,2-ETHANEDIOL
2MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN3Ligand/IonZINC ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MLY-1Mod. Amino AcidN-DIMETHYL-LYSINE
3SAH-1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:32 , TYR A:114 , GLU A:117 , GLY A:120 , ALA A:121 , PHE A:160 , ALA A:179 , ASN A:182 , HIS A:183 , TYR A:217 , PHE A:222 , CYS A:229 , GLU A:230 , CYS A:231 , EDO A:1251 , HOH A:2015 , HOH A:2053 , MLY C:20BINDING SITE FOR RESIDUE SAH A1247
02AC2SOFTWARECYS A:185 , CYS A:229 , CYS A:231 , CYS A:234BINDING SITE FOR RESIDUE ZN A1248
03AC3SOFTWAREHIS A:92 , CYS A:95 , CYS A:141 , HOH A:2033BINDING SITE FOR RESIDUE ZN A1249
04AC4SOFTWAREALA A:99 , PHE A:100 , LEU A:101 , PRO A:102 , SER A:104 , GLY A:105 , PHE A:106 , THR A:126 , EDO A:1257BINDING SITE FOR RESIDUE EDO A1250
05AC5SOFTWARETYR A:114 , SER A:115 , MET A:116 , GLU A:230 , SAH A:1247BINDING SITE FOR RESIDUE EDO A1251
06AC6SOFTWARECYS A:95 , ARG A:98 , ALA A:99 , LEU A:137 , VAL A:139 , HOH A:2034BINDING SITE FOR RESIDUE EDO A1252
07AC7SOFTWAREPHE A:29 , ARG A:30 , ASN A:119 , HOH A:2013BINDING SITE FOR RESIDUE EDO A1253
08AC8SOFTWAREASP A:24 , GLY A:28 , PHE A:29 , ARG A:30 , GLN A:45 , HOH A:2012BINDING SITE FOR RESIDUE EDO A1254
09AC9SOFTWAREGLU A:150 , LEU A:153 , ARG C:19BINDING SITE FOR RESIDUE EDO A1255
10BC1SOFTWARETHR A:91 , ARG A:98 , HOH A:2031 , HOH A:2032BINDING SITE FOR RESIDUE EDO A1256
11BC2SOFTWAREPRO A:102 , GLY A:105 , THR A:126 , ARG A:127 , EDO A:1250 , HOH A:2036BINDING SITE FOR RESIDUE EDO A1257
12BC3SOFTWARECYS B:185BINDING SITE FOR RESIDUE ZN B1219
13BC4SOFTWAREASP B:16 , VAL B:36 , SER B:37 , PRO B:38 , TYR B:77BINDING SITE FOR RESIDUE EDO B1220
14BC5SOFTWARELEU B:42 , ARG B:43 , GLN B:45 , LEU B:48 , HOH B:2004BINDING SITE FOR RESIDUE EDO B1221
15BC6SOFTWARETYR B:26 , ARG B:49 , ARG B:59 , LEU B:101BINDING SITE FOR RESIDUE EDO B1222
16BC7SOFTWAREPRO B:187 , CYS B:189 , LYS B:190 , PHE B:191 , CYS B:215 , PHE B:216BINDING SITE FOR RESIDUE EDO B1223
17BC8SOFTWAREHIS B:46 , ARG B:49 , SER B:50 , GLU B:103 , SER B:104 , PHE B:106 , TRP B:129 , LEU B:135 , GLU B:136 , LEU B:137BINDING SITE FOR RESIDUE EDO B1224
18BC9SOFTWAREASP B:60 , ALA B:63 , ARG B:66BINDING SITE FOR RESIDUE EDO B1225
19CC1SOFTWAREASP B:60 , LEU B:61 , GLU B:62 , VAL B:124 , SER B:125 , HOH B:2020BINDING SITE FOR RESIDUE EDO B1226
20CC2SOFTWAREGLU B:117 , ALA B:121 , ASN B:182BINDING SITE FOR RESIDUE EDO B1227

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AU7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg C:23 -Asp C:24

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AU7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5C_MOUSE104-218
 		  2A:104-218
B:104-218
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5C_MOUSE104-218
 		  1A:104-218
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5C_MOUSE104-218
 		  1-
B:104-218

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSMUST000000877141ENSMUSE00000906044chr13:21826903-21827329427H4_MOUSE1-1241241C:17-25 (gaps)35

(-) 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:243
 aligned with KMT5C_MOUSE | Q6Q783 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:243
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   
          KMT5C_MOUSE     4 DRVTARELCENDDLATSLVLDPYLGFRTHKMNVSPVPTLRRQHHLRSALEAFLRQRDLEAAFRALTLGGWMAHYFQSRAPRQEAALKTHIFCYLRAFLPESGFTILPCTRYSMETNGAKIVSTRAWKKNEKLELLVGCIAELREEDEDLLRAGENDFSIMYSTRKRSAQLWLGPAAFINHDCKPNCKFVPSDGNTACVKVLRDIEPGDEVTCFYGEGFFGEKNEHCECYTCERKGEGAFRLQP 246
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.eeeeee........eeeeee........eeeeeeeeeee.hhhhhhhh........eeee....eeeeeehhhhhhee.....eeeee....eeeeee..........ee...............hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------SET  PDB: A:104-218 UniProt: 104-218                                                                               ---------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4au7 A   4 DRVTARELCENDDLATSLVLDPYLGFRTHKMNVSPVPTLRRQHHLRSALEAFLRQRDLEAAFRALTLGGWMAHYFQSRAPRQEAALKTHIFCYLRAFLPESGFTILPCTRYSMETNGAKIVSTRAWKKNEKLELLVGCIAELREEDEDLLRAGENDFSIMYSTRKRSAQLWLGPAAFINHDCKPNCKFVPSDGNTACVKVLRDIEPGDEVTCFYGEGFFGEKNEHCECYTCERKGEGAFRLQP 246
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243   


Chain B from PDB  Type:PROTEIN  Length:209
 aligned with KMT5C_MOUSE | Q6Q783 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:214
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214    
          KMT5C_MOUSE     5 RVTARELCENDDLATSLVLDPYLGFRTHKMNVSPVPTLRRQHHLRSALEAFLRQRDLEAAFRALTLGGWMAHYFQSRAPRQEAALKTHIFCYLRAFLPESGFTILPCTRYSMETNGAKIVSTRAWKKNEKLELLVGCIAELREEDEDLLRAGENDFSIMYSTRKRSAQLWLGPAAFINHDCKPNCKFVPSDGNTACVKVLRDIEPGDEVTCFYG 218
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.eeeee..........eeeee........eeeeeeeeeee.hhhhhhhh........ee.-----..eeeehhhhhhee.....eeeee....eeeeee..........ee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------SET  PDB: B:104-218 UniProt: 104-218                                                                                PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4au7 B   5 RVTARELCENDDLATSLVLDPYLGFRTHKMNVSPVPTLRRQHHLRSALEAFLRQRDLEAAFRALTLGGWMAHYFQSRAPRQEAALKTHIFCYLRAFLPESGFTILPCTRYSMETNGAKIVSTRAWKKNEKLELLVGCIAELREEDEDLLRAGENDFSIMY-----SAQLWLGPAAFINHDCKPNCKFVPSDGNTACVKVLRDIEPGDEVTCFYG 218
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164     | 174       184       194       204       214    
                                                                                                                                                                                         164   170                                                


Chain C from PDB  Type:PROTEIN  Length:9
 aligned with H4_MOUSE | P62806 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:35
                                    27        37        47     
             H4_MOUSE    18 RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIY  52
               SCOP domains ----------------------------------- SCOP domains
               CATH domains ----------------------------------- CATH domains
               Pfam domains ----------------------------------- Pfam domains
         Sec.struct. author ...eee..--------------------------. Sec.struct. author
                 SAPs(SNPs) ----------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:17-25 (gaps)       Transcript 1
                 4au7 C  17 RHRkVLRD--------------------------Y  25
                               |   | -         -         -    |
                               |  24                         25
                              20-MLY
   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  (0, 0)

(no "SCOP Domain" information available for 4AU7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AU7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AU7)

(-) Gene Ontology  (35, 38)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KMT5C_MOUSE | Q6Q783)
molecular function
    GO:0042799    histone methyltransferase activity (H4-K20 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H4 L-lysine (position 20) = S-adenosyl-L-homocysteine + histone H4 N6-methyl-L-lysine (position 20). This reaction is the addition of a methyl group onto lysine at position 20 of the histone H4 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:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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.
biological process
    GO:0034773    histone H4-K20 trimethylation    The modification of histone H4 by addition of three methyl groups to lysine at position 20 of the histone.
    GO:0016571    histone methylation    The modification of histones by addition of methyl groups.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000780    condensed nuclear chromosome, centromeric region    The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. 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:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    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:0005721    pericentric heterochromatin    Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.

Chain C   (H4_MOUSE | P62806)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0032776    DNA methylation on cytosine    The covalent transfer of a methyl group to C-5 or N-4 of cytosine in a DNA molecule.
    GO:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    GO:0006352    DNA-templated transcription, initiation    Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0045653    negative regulation of megakaryocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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  4au7
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  H4_MOUSE | P62806
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  KMT5C_MOUSE | Q6Q783
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  H4_MOUSE | P62806
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        H4_MOUSE | P62806: 1f66 1kx4 1kx5 1m18 1m19 1m1a 1s32 1u35 2wp2 4dow 5b1l 5b1m

(-) Related Entries Specified in the PDB File

1f66 2.6 A CRYSTAL STRUCTURE OF A NUCLEOSOME CORE PARTICLECONTAINING THE VARIANT HISTONE H2A.Z
1u35 CRYSTAL STRUCTURE OF THE NUCLEOSOME CORE PARTICLECONTAINING THE HISTONE DOMAIN OF MACROH2A
2wp2 STRUCTURE OF BRDT BROMODOMAIN BD1 BOUND TO A DIACETYLATED HISTONE H4 PEPTIDE.