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(-) Description

Title :  CRYSTAL STRUCTURE OF KRYPTONITE IN COMPLEX WITH MCHH DNA, H3(1-15) PEPTIDE 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 :  2.00
Chains :  Asym./Biol. Unit :  A,C,D,P
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
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: BL21(DE3) RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FUNCTIONAL FRAGMENT
    Gene: SUVH4, KYP, SDG33, SET33, AT5G13960, MAC12.7
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: HISTONE 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'-GGTACT(5CM)ATCAGTAT-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA 5'-ACTGATGAGTACCAT-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - HISTONE H3
    Chains: P
    Engineered: YES
    Fragment: UNP RESIDUES 2-16
    Organism Common: CLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Other Details: SAH WAS ORDERED FROM SIGMA.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ACDP

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  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:456 , GLY A:457 , TRP A:458 , GLU A:492 , TYR A:493 , ARG A:548 , ASN A:551 , HIS A:552 , TYR A:593 , ALA A:611 , CYS A:612 , TYR A:613 , CYS A:614 , LYS P:9BINDING SITE FOR RESIDUE SAH A 801
2AC2SOFTWARECYS A:383 , CYS A:397 , CYS A:425 , CYS A:429BINDING 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:395BINDING SITE FOR RESIDUE ZN A 804
5AC5SOFTWARECYS A:554 , CYS A:612 , CYS A:614 , CYS A:619BINDING SITE FOR RESIDUE ZN A 805
6AC6SOFTWARESER A:418 , ARG A:419 , ASP A:420 , TYR A:475 , GLU A:492 , ILE A:494 , PHE A:495 , GLU A:496 , TYR A:591 , TYR A:593 , GLY A:594 , TYR A:595 , SAH A:801BINDING SITE FOR CHAIN P OF HISTONE H3

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:195 -Pro A:196
2Gly A:602 -Pro A:603

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QEO)

(-) 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:472
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh....................ee.hhhhhhhh.........eeeehhhhh.........eeeeeee.......eee..eeeee....................hhhhhhhhhhhhh..eeeeeeee.......eeeeeeeeeeeeeeeeee.....eeeeeeeee.............eee.............ee..............ee....ee........................hhhhhhh.....ee.....ee......ee...........hhhhhhhh.....eeeee.....eeeee........eeee...eeee.hhh...eee.....eeee...eehhhhhhee.....eeeeeee....hhhhheeeeee..........ee........ee.....ee................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qeo A  99 LEPHLKVTKCLRLFNKQYLLCVQAKLSRPDLKGVTEMIKAKAILYPRKIIGDLPGIDVGHRFFSRAEMCAVGFHNHWLNGIDYMSMEYEKEYSNYKLPLAVSIVMSGQYEDDLDNADTVTYTGQGGHNLTGNKRQIKDQLLERGNLALKHCCEYNVPVRVTRGHNCKSSYTKRVYTYDGLYKVEKFWAQKGVSGFTVYKYRLKRLEGQPELTTDIEGLVCEDISGGLEFKGIPATNRVDDSPVSPTSGFTYIKSLIIEPNVIIPKSSTGCNCRGSCTDSKKCACAKLNGGNFPYVDLNDGRLIESRDVVFECGPHCGCGPKCVNRTSQKRLRFNLEVFRSAKKGWAVRSWEYIPAGSPVCEYIGVVRRTADVNEYIFEIDCPEFCIDAGSTGNFARFINHSCEPNLFVQCVLSSHQDIRLARVVLFAADNISPMQELTYDYGYALDSVHGPDGKVKQLACYCGALNCRKRLY 624
                                   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   ||  333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483 ||    498||     542       552       562       572       582       592       602       612       622  
                                                                                                                                                                                                                                               312|                                                                                                                                                          485|     499|                                                                                          
                                                                                                                                                                                                                                                328                                                                                                                                                           491      534                                                                                          


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


Chain D from PDB  Type:DNA  Length:13
                                             
                 4qeo D   3 TGATGAGTACCAT  15
                                    12   


Chain P from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4qeo P   9 KSTGGKA  15
   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 4QEO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (23, 25)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q92133_XENLA | Q92133: 2hue 3gv6
        SUVH4_ARATH | Q8GZB6: 4qen 4qep
UniProtKB/TrEMBL
        Q92133_XENLA | Q92133: 2l11 2l12 2l1b 3gl6 3h91 3me9 3mea 3met 3meu 3mev 3o7a 4hsu

(-) Related Entries Specified in the PDB File

4qen THE SAME PROTEIN COMPLEXED WITH MCHH DNA AND SAH
4qep