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(-) Description

Title :  CRYSTAL STRUCTURE OF KRYPTONITE IN COMPLEX WITH MCHG DNA AND SAH
 
Authors :  J. Du, S. Li, D. J. Patel
Date :  17 May 14  (Deposition) - 30 Jul 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,C,D
Keywords :  Sra, Set, Histone Methylation, Methylated Dna, Methylation, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Du, L. M. Johnson, M. Groth, S. Feng, C. J. Hale, S. Li, A. A. Vashisht, J. Gallego-Bartolome, J. A. Wohlschlegel, D. J. Patel, S. E. Jacobsen
Mechanism Of Dna Methylation-Directed Histone Methylation B Kryptonite.
Mol. Cell V. 55 495 2014
PubMed-ID: 25018018  |  Reference-DOI: 10.1016/J.MOLCEL.2014.06.009

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC SUVH4
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-SUMO
    Expression System StrainBL21(DE3) RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentFUNCTIONAL FRAGMENT
    GeneSUVH4, KYP, SDG33, SET33, AT5G13960, MAC12.7
    Organism CommonMOUSE-EAR CRESS,THALE-CRESS
    Organism ScientificARABIDOPSIS THALIANA
    Organism Taxid3702
    SynonymHISTONE H3-K9 METHYLTRANSFERASE 4, H3-K9-HMTASE 4, PROTEIN KRYPTONITE, PROTEIN SET DOMAIN GROUP 33, SUPPRESSOR OF VARIEGATION 3- 9 HOMOLOG PROTEIN 4, SU(VAR)3-9 HOMOLOG PROTEIN 4
 
Molecule 2 - DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM) P*AP*GP*CP*AP*GP*TP*AP*T)-3')
    ChainsC
    EngineeredYES
    SyntheticYES
 
Molecule 3 - DNA (5'-D(*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)- 3')
    ChainsD
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ACD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3ZN4Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:456 , GLY A:457 , TRP A:458 , TYR A:493 , ARG A:548 , ASN A:551 , HIS A:552 , TYR A:593 , CYS A:612 , TYR A:613BINDING SITE FOR RESIDUE SAH A 801
2AC2SOFTWARECYS A:383 , CYS A:397 , CYS A:425 , CYS A:429 , ZN A:804BINDING SITE FOR RESIDUE ZN A 802
3AC3SOFTWARECYS A:389 , CYS A:425 , CYS A:431 , CYS A:435BINDING SITE FOR RESIDUE ZN A 803
4AC4SOFTWARECYS A:383 , CYS A:385 , CYS A:389 , CYS A:395 , ZN A:802BINDING SITE FOR RESIDUE ZN A 804
5AC5SOFTWARECYS A:554 , CYS A:612 , CYS A:614 , CYS A:619BINDING SITE FOR RESIDUE ZN A 805

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:195 -Pro A:196

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QEP)

(-) Exons   (0, 0)

(no "Exon" information available for 4QEP)

(-) Sequences/Alignments

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:467
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....................ee.hhhhhhhh.........eeeehhhhh.........eeeeeee.......ee...eeeee....................hhhhhhhhhhhhh..eeeeeeee.......eeeeeeeeeeeeeeeeee.....eeeeeeeee............eee.............ee..............ee....ee........................hhhhhhh.....ee.....ee.....eee...........hhhhhhhh.....eeeee.....eeeee........eeee...eeee.hhh...eee.....eeee...eehhhhhhee.....eeeeeee....hhhhheeeeee..........ee............................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qep A  99 LEPHLKVTKCLRLFNKQYLLCVQAKLSRPDLKGVTEMIKAKAILYPRKIIGDLPGIDVGHRFFSRAEMCAVGFHNHWLNGIDYMSMEYEKEYSNYKLPLAVSIVMSGQYEDDLDNADTVTYTGQGGHNLTGNKRQIKDQLLERGNLALKHCCEYNVPVRVTRGHNCKSSYTKRVYTYDGLYKVEKFWAQKGVSGFTVYKYRLKRLEGQPELTTDEGLVCEDISGGLEFKGIPATNRVDDSPVSPTSGFTYIKSLIIEPNVIIPKSSTGCNCRGSCTDSKKCACAKLNGGNFPYVDLNDGRLIESRDVVFECGPHCGCGPKCVNRTSQKRLRFNLEVFRSAKKGWAVRSWEYIPAGSPVCEYIGVVRRTADVNEYIFEIDCPEFCIDAGSTGNFARFINHSCEPNLFVQCVLSSHQDIRLARVVLFAADNISPMQELTYDYGYALDSVHKVKQLACYCGALNCRKRLY 624
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   ||  334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484||     499|      543       553       563       573       583       593       607       617       
                                                                                                                                                                                                                                               312|                                                                                                                                                         485|     499|                                                                601|                  
                                                                                                                                                                                                                                                329                                                                                                                                                          491      534                                                                 606                  

Chain C from PDB  Type:DNA  Length:11
                                           
                 4qep C   1 GGTACTcAGCA  11
                                  | 10 
                                  7-5CM

Chain D from PDB  Type:DNA  Length:13
                                             
                 4qep D   3 TGCTGAGTACCAT  15
                                    12   

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  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 4QEP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu A:195 - Pro A:196   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SUVH4_ARATH | Q8GZB64qen 4qeo

(-) Related Entries Specified in the PDB File

4qen THE SAME PROTEIN IN COMPLEX MCHH DNA AND SAH.
4qeo THE SAME PROTEIN IN COMPLEX MCHH DNA, H3(1-15) PEPTIDE AND SAH.