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(-) Description

Title :  CRYSTAL STRUCTURE OF ZEA MAYS ZMET2 IN COMPLEX H3(1-15)K9ME2 PEPTIDE AND SAH
 
Authors :  J. Du, D. J. Patel
Date :  27 Jun 12  (Deposition) - 17 Oct 12  (Release) - 13 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Chromodomain, Bah Domain, Dna Methyltransferase Domain, Dna Methyltransferase, H3K9Me2 Binding, Methylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Du, X. Zhong, Y. V. Bernatavichute, H. Stroud, S. Feng, E. Caro, A. A. Vashisht, J. Terragni, H. G. Chin, A. Tu, J. Hetzel, J. A. Wohlschlegel, S. Pradhan, D. J. Patel, S. E. Jacobsen
Dual Binding Of Chromomethylase Domains To H3K9Me2-Containing Nucleosomes Directs Dna Methylation In Plants.
Cell(Cambridge, Mass. ) V. 151 167 2012
PubMed-ID: 23021223  |  Reference-DOI: 10.1016/J.CELL.2012.07.034

(-) Compounds

Molecule 1 - DNA (CYTOSINE-5)-METHYLTRANSFERASE 1
    ChainsA, B
    EC Number2.1.1.37
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-SUMO
    Expression System StrainBL21(DE3) RIL
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 130-912
    GeneMET2A, ZMET2
    Organism CommonMAIZE
    Organism ScientificZEA MAYS
    Organism Taxid4577
    SynonymCHROMOMETHYLASE 1, DNA CYTOSINE METHYLTRANSFERASE MET2A, ZEA METHYLTRANSFERASE2, ZMET2
 
Molecule 2 - H3 PEPTIDE
    ChainsP
    EngineeredYES
    FragmentHISTONE H3 PEPTIDE, UNP RESIDUES 16-30
    Other DetailsH3 PEPTIDE WAS SYNTHESIZED
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:347 , SER A:348 , GLY A:351 , GLY A:352 , ASP A:375 , PHE A:376 , ASN A:377 , GLU A:396 , LYS A:397 , ALA A:398 , PRO A:516 , GLN A:540 , ALA A:852 , VAL A:853BINDING SITE FOR RESIDUE SAH A 1000
2AC2SOFTWARETYR B:347 , GLY B:349 , CYS B:350 , GLY B:352 , MET B:353 , ASP B:375 , PHE B:376 , ASN B:377 , GLU B:396 , LYS B:397 , ALA B:398 , PRO B:516 , GLN B:540 , GLU B:559 , ASN B:851 , ALA B:852 , VAL B:853BINDING SITE FOR RESIDUE SAH B 1000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FT2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FT2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FT2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FT2)

(-) Exons   (0, 0)

(no "Exon" information available for 4FT2)

(-) 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:674
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhh.........ee..eeee..eeee...eeee........eeeeeeeeeee..eeeeeeeeeee.........................eeeeeeeeee.....ee..eee.......hhhhhhhhh..eee.eeee....eeee.....eeeeee....hhhhhhhhhhhhhhh..eeeeeeee.hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh....eeeeeee........eeeeee....hhhhheeee......hhhhhhhhhhhhhhhh.........eeee.........hhhhhhhhhhhhhhh...eeeeeehhhhhh..hhhhhhhhhhhhhh....eeeeee..........eeeeee..........ee...................................hhhhhhh.....................hhhhhhhh.hhhhhh.......................hhhhhhhhhhh........................................hhhhhhhhhhh.....................hhhhhh..........hhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......ee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ft2 A 132 DHEPEFIGSPVAADEARSNWPKRYGLKARCHYRSAKVDNVVYCLGDDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAEDTVINSLVSISVDGHKHDPRRVFLSEEKNDNVLDCIISKVKIVHVDPNMDPKAKAQLIESCDLYYDMSYSVAYSTFANISTRTATLLDLYSGCGGMSTGLCLGAALSGLKLETRWAVDFNSFACQSLKYNHPQTEVRNEKADEFLALLKEWAVLCKKYVVVEKLVGICYGGSDRENGIYFKVQWEGYGPEEDTWEPIDNLSDCPQKIREFVQEGHKRKILPLPGDVDVICGGPPCQKDEKNKQMVTFMDIVAYLKPKYVLMENVVDILKFADGYLGKYALSCLVAMKYQARLGMMVAGCYGLPQFRMRVFLWGALSSMVLPKYPLPTYDVVVRGGAPNAFSQCMVAYDETQKPSLKKALLLGDAISDLPKVQNHQPNDVMEYGGSPKTEFQRYIRLSRKDMLDWSFGEGAGPDEGKLLDHQPLRLNNDDYERVQQIPVKKGANFRDLKGVRVGANNIVEWDPEIERVKLSSGKPLVPDYAMSFIKGKSLKPFGRLWWDETVPTVVTRAEPHNQVIIHPTQARVLTIRENARLQGFPDYYRLFGPIKEKYIQVGNAVAVPVARALGYCLGQAYLGESEGSDPLYQLPPSF 886
                                   141       151    || 174       184       194       204       214       224       234       244       254       264       274       284       294       304    || 342       352       362       372       382       392       402       412   ||  447       457       467       477       487       497       507       517||     542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882    
                                                  156|                                                                                                                                        309|                                                                           416|                                                                         518|                                                                                                                                                                                                                                                                                                                                                                
                                                   170                                                                                                                                         338                                                                            442                                                                          534                                                                                                                                                                                                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:670
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhh..eeeee.eeee..eeee...eeee........eeeeeeeeeee....eeeeeeeeee.......................eeeeeeeeeee...eeee..eee.hhhhh.hhhhhhhhhh.eee..eee....eee...eeeeeee....hhhhhhhhhhhhhhh.eeeeeeeee.hhhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhhhhh....eeeeeeeee........eeeeeee.........eee.hhhhhhhhhhhhhhhhhhhhh.........eee..........hhhhhhhhhhhhhhh..eeeeee.hhhhhh..hhhhhhhhhhhhhh..eeeeeeee.hhhh.....eeeeeeee........ee...................................hhhhhhh............ee.......hhhhhhhh.....................ee.......hhhhhhhhhhh......hhhhh............................hhhhhh...........................hhhhhh..........hhhhhhhhh..........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.......ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ft2 B 134 EPEFIGSPVAADEARSNWPKRYLKARCHYRSAKVDNVVYCLGDDVYVKAGENEADYIGRITEFFEGTDQCHYFTCRWFFRAEDTVINSLVSISVDGHKHDPRRVFLSEEKNDNVLDCIISKVKIVHVDPNMDPKAKAQLIESCDLYYDMSYSVAYSTFANTRTATLLDLYSGCGGMSTGLCLGAALSGLKLETRWAVDFNSFACQSLKYNHPQTEVRNEKADEFLALLKEWAVLCKKYVEFVVEKLVGICYGGSDRENGIYFKVQWEGYGPEEDTWEPIDNLSDCPQKIREFVQEGHKRKILPLPGDVDVICGGPPCQKDEKNKQMVTFMDIVAYLKPKYVLMENVVDILKFADGYLGKYALSCLVAMKYQARLGMMVAGCYGLPQFRMRVFLWGALSSMVLPKYPLPTYDVVVRGGAPNAFSQCMVAYDETQKPSLKKALLLGDAISDLPKVQNHQPNDVMEYGGSPKTEFQRYIRLSRKDMLDWSFGEGAGPDEGKLLDHQPLRLNNDDYERVQQIPVKKGANFRDLKGVRVGANNIVEWDPEIERVKLSSGKPLVPDYAMSFIKGKSLKPFGRLWWDETVPTVVTRAEPHNQVIIHPTQARVLTIRENARLQGFPDYYRLFGPIKEKYIQVGNAVAVPVARALGYCLGQAYLGESEGSDPLYQLPPS 885
                                   143       153 ||    177       187       197       207       217       227       237       247       257       267       277       287       297       307|      347       357       367       377       387       397       407       440       450       460       470       480       490       500       510       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885
                                               155|                                                                                                                                      307|                                                                           416|                                                                           518|                                                                                                                                                                                                                                                                                                                                                               
                                                170                                                                                                                                       338                                                                            440                                                                            534                                                                                                                                                                                                                                                                                                                                                               

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
                 4ft2 P   5 QTARkST  11
                                |  
                                9-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 4FT2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FT2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FT2)

(-) Gene Ontology  (36, 44)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CMT1_MAIZE | Q9AXT84fsx 4ft4
        H31_HUMAN | P684311cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5v22 5va6
        H32_ARATH | P592264ft4 4iur 4iut 4iuu 4iuv 5hh7 5vah 5vbc

(-) Related Entries Specified in the PDB File

4fsx THE SAME PROTEIN IN COMPLEX WITH H3K9ME2 PEPTIDE
4ft4