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(-) Description

Title :  CRYSTAL STRUCTURE OF THE SET DOMAIN OF HUMAN HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H1 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE
 
Authors :  R. Lam, H. Zeng, P. Loppnau, C. Bountra, J. Weigelt, C. H. Arrowsmith, A. M. Edwards, J. Min, H. Wu, Structural Genomics Consortium (Sgc)
Date :  30 May 11  (Deposition) - 06 Jul 11  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Set Domain, Histone Methyltransferase, Transcription Regulation, Histone Lysine, Sam, Methylation, Nucleus, Chromosome, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Wu, A. Siarheyeva, H. Zeng, R. Lam, A. Dong, X. H. Wu, Y. Li, M. Schapira, M. Vedadi, J. Min
Crystal Structures Of The Human Histone H4K20 Methyltransferases Suv420H1 And Suv420H2.
Febs Lett. V. 587 3859 2013
PubMed-ID: 24396869

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SUV420H1
    Chains: A, B
    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: 562
    Expression System Vector Type: PLASMID
    Fragment: SET DOMAIN
    Gene: CGI-85, KMT5B, SUV420H1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LYSINE N-METHYLTRANSFERASE 5B, SUPPRESSOR OF VARIEGATION 4- 20 HOMOLOG 1, SU(VAR)4-20 HOMOLOG 1, SUV4-20H1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SAM1Ligand/IonS-ADENOSYLMETHIONINE
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:275 , CYS A:319 , CYS A:321 , CYS A:324BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREHOH A:31 , HIS A:98 , TYR A:203 , SER A:205 , GLU A:206 , GLY A:209 , ALA A:210 , PHE A:250 , ALA A:269 , PHE A:270 , ILE A:271 , ASN A:272 , HIS A:273 , TYR A:307 , PHE A:312 , CYS A:319 , GLU A:320 , CYS A:321 , HOH A:436 , ARG B:257BINDING SITE FOR RESIDUE SAM A 500
3AC3SOFTWARECYS B:275 , CYS B:319 , CYS B:321 , CYS B:324BINDING SITE FOR RESIDUE ZN B 400
4AC4SOFTWAREARG A:257 , HOH A:352 , HOH B:14 , HOH B:52 , HIS B:98 , TYR B:203 , SER B:205 , GLU B:206 , GLY B:209 , ALA B:210 , PHE B:250 , ALA B:269 , PHE B:270 , ILE B:271 , ASN B:272 , HIS B:273 , TYR B:307 , PHE B:312 , CYS B:319 , GLU B:320 , CYS B:321BINDING SITE FOR RESIDUE SAM B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3S8P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S8P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3S8P)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5B_HUMAN193-308
 		  2A:193-308
B:193-308
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5B_HUMAN193-308
 		  1A:193-308
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5B_HUMAN193-308
 		  1-
B:193-308

(-) Exons   (0, 0)

(no "Exon" information available for 3S8P)

(-) 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:233
 aligned with KMT5B_HUMAN | Q4FZB7 from UniProtKB/Swiss-Prot  Length:885

    Alignment length:263
                                    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   
          KMT5B_HUMAN    72 MSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFSHNNPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEHVFIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENMLLRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYYGDGFFGENNEFCECYTCERRGTGAFKS 334
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh........------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.eeeeee........eeeeee........eeeeeeeeeeeehhhhhhhhh........eeee....eeeeeehhhhhhee.....eeeeeee..eeeeee..........ee.......hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------SET  PDB: A:193-308 UniProt: 193-308                                                                                -------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s8p A  72 mSAKELCENDDLATSLVLDPYLGFQTHKmNT------------------------------RQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKmQEKLFKEHVFIYLRmFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENmLLRHGENDFSVmYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYYGDGFFGENNEFCECYTCERRGTGAFKS 334
                            |       81        91       101|        -         -         - |     141       151       161       171 |     181      |191       201       211       221       231       241       251 |     261       271       281       291       301       311       321       331   
                            |                         100-MSE                          133                                     173-MSE        188-MSE                                              241-MSE     253-MSE                                                                             
                           72-MSE                       102                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with KMT5B_HUMAN | Q4FZB7 from UniProtKB/Swiss-Prot  Length:885

    Alignment length:263
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
          KMT5B_HUMAN    71 GMSAKELCENDDLATSLVLDPYLGFQTHKMNTSAFPSRSSRHFSKSDSFSHNNPVRFRPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEHVFIYLRMFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENMLLRHGENDFSVMYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYYGDGFFGENNEFCECYTCERRGTGAFK 333
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh........-------------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhhhhhh......eeeeee........eeeeee........eeeeeeeeeeeehhhhhhhhh........eeee....eeeeeehhhhhhee.....eeeeeee..eeeeee..........ee.......hhhhh...hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------SET  PDB: B:193-308 UniProt: 193-308                                                                                ------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s8p B  71 GmSAKELCENDDLATSLVLDPYLGFQTHKmNT-------------------------RPIKGRQEELKEVIERFKKDEHLEKAFKCLTSGEWARHYFLNKNKmQEKLFKEHVFIYLRmFATDSGFEILPCNRYSSEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENmLLRHGENDFSVmYSTRKNCAQLWLGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYYGDGFFGENNEFCECYTCERRGTGAFK 333
                             |      80        90       100 |       -         -       130       140       150       160       170  |    180       190       200       210       220       230       240|      250  |    260       270       280       290       300       310       320       330   
                            72-MSE                     100-MSE                     128                                          173-MSE        188-MSE                                              241-MSE     253-MSE                                                                            
                                                         102
   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 3S8P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S8P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S8P)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KMT5B_HUMAN | Q4FZB7)
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:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    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: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.

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