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(-) Description

Title :  METHYLTRANSFERASE DOMAIN OF HUMAN EUCHROMATIC HISTONE METHYLTRANSFERASE 1, MUTANT Y1211A
 
Authors :  A. Dong, H. Zeng, J. R. Walker, K. Islam, C. Bountra, C. H. Arrowsmith, A. M. Edwards, M. Lou, J. Min, H. Wu, Structural Genomics Consortium
Date :  28 Nov 12  (Deposition) - 19 Dec 12  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D,K
Keywords :  Ne-Allyl Peptide, Structural Genomics Consortium, Transferase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Islam, Y. Chen, H. Wu, I. R. Bothwell, G. J. Blum, H. Zeng, A. Dong, W. Zheng, J. Min, H. Deng, M. Luo
Defining Efficient Enzyme-Cofactor Pairs For Bioorthogonal Profiling Of Protein Methylation.
Proc. Natl. Acad. Sci. Usa V. 110 16778 2013
PubMed-ID: 24082136  |  Reference-DOI: 10.1073/PNAS.1216365110

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE EHMT1
    ChainsA, B
    EC Number2.1.1.-, 2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21-V2R-PRARE2
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneEHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 1, EU- HMTASE1, G9A-LIKE PROTEIN 1, GLP, GLP1, HISTONE H3-K9 METHYLTRANSFERASE 5, H3-K9-HMTASE 5, LYSINE N-METHYLTRANSFERASE 1D
 
Molecule 2 - H3K9 NE-ALLYL PEPTIDE
    ChainsC, D
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES
 
Molecule 3 - UNKNOWN PEPTIDE
    ChainsK
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCDK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 34)

Asymmetric/Biological Unit (6, 34)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2LDH2Mod. Amino AcidN~6~-ETHYL-L-LYSINE
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4UNK10Mod. Amino Acid
5UNX9Ligand/IonUNKNOWN ATOM OR ION
6ZN8Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:1105 , GLY A:1106 , TRP A:1107 , SER A:1141 , TYR A:1142 , ARG A:1166 , PHE A:1167 , ILE A:1168 , ASN A:1169 , HIS A:1170 , PHE A:1215 , LYS A:1219 , PHE A:1223 , CYS A:1225 , ARG A:1226 , HOH A:3151 , HOH A:3173 , HOH A:3215 , HOH A:3314 , LDH C:2009BINDING SITE FOR RESIDUE SAH A 3001
02AC2SOFTWARECYS A:1031 , CYS A:1044 , CYS A:1074 , CYS A:1078BINDING SITE FOR RESIDUE ZN A 3002
03AC3SOFTWARECYS A:1037 , CYS A:1074 , CYS A:1080 , CYS A:1084BINDING SITE FOR RESIDUE ZN A 3003
04AC4SOFTWARECYS A:1031 , CYS A:1033 , CYS A:1037 , CYS A:1042BINDING SITE FOR RESIDUE ZN A 3004
05AC5SOFTWARECYS A:1172 , CYS A:1225 , CYS A:1227 , CYS A:1232BINDING SITE FOR RESIDUE ZN A 3005
06AC6SOFTWAREASN A:1013 , ILE A:1021 , ARG A:1023 , HOH B:3266BINDING SITE FOR RESIDUE GOL A 3006
07AC7SOFTWARECYS A:1033 , ILE A:1034 , ASP A:1035 , SER A:1039 , ASN A:1041 , HOH A:3365 , LEU B:1047 , LEU B:1070 , PHE B:1072BINDING SITE FOR RESIDUE GOL A 3007
08AC8SOFTWAREMET B:1105 , GLY B:1106 , TRP B:1107 , SER B:1141 , TYR B:1142 , ARG B:1166 , PHE B:1167 , ASN B:1169 , HIS B:1170 , PHE B:1223 , CYS B:1225 , ARG B:1226 , HOH B:3206 , LDH D:2009BINDING SITE FOR RESIDUE SAH B 3001
09AC9SOFTWARECYS B:1031 , CYS B:1044 , CYS B:1074 , CYS B:1078BINDING SITE FOR RESIDUE ZN B 3002
10BC1SOFTWARECYS B:1037 , CYS B:1074 , CYS B:1080 , CYS B:1084BINDING SITE FOR RESIDUE ZN B 3003
11BC2SOFTWARECYS B:1031 , CYS B:1033 , CYS B:1037 , CYS B:1042BINDING SITE FOR RESIDUE ZN B 3004
12BC3SOFTWARECYS B:1172 , CYS B:1225 , CYS B:1227 , CYS B:1232BINDING SITE FOR RESIDUE ZN B 3005
13BC4SOFTWAREARG A:1023 , HOH A:3123 , ARG B:1023 , LEU B:1128 , HOH B:3155BINDING SITE FOR RESIDUE GOL B 3006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I51)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I51)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I51)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I51)

(-) Exons   (0, 0)

(no "Exon" information available for 4I51)

(-) 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:261
                                                                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.............eee...........ee....ee........hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eee........eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4i51 A  975 VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNKDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDAGERFWDIKGKLFSCRCGSPKCRHS 1235
                                   984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234 

Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.............eee...........ee..............hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhhhh.....eee...eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4i51 B  973 SPVERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDAGERFWDIKGKLFSCRCGSPKCRHS 1235
                                   982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142    ||1157      1167      1177      1187      1197      1207      1217      1227        
                                                                                                                                                                                                       1147|                                                                                  
                                                                                                                                                                                                        1153                                                                                  

Chain C from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......ee. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                4i51 C 2003 TKQTARkST 2011
                                  |  
                               2009-LDH

Chain D 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
                4i51 D 2005 QTARkST 2011
                                |  
                                |  
                             2009-LDH

Chain K from PDB  Type:PROTEIN  Length:10
                                           
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .....hhhhh Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                4i51 K 1952 xxxxxxxxxx 1967
                            ||||||1967
                            |||||1966-UNK
                         1952-UNK|1967-UNK
                          1953-UNK||  
                           1954-UNK|  
                            1955-UNK  
                             1959-UNK 
                              1960-UNK
                               1961-UNK
                                1962-UNK

   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 4I51)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I51)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I51)

(-) Gene Ontology  (51, 55)

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
        EHMT1_HUMAN | Q9H9B12igq 2rfi 3b7b 3b95 3fpd 3hna 3mo0 3mo2 3mo5 3sw9 3swc 5ttg 5tuz 5vsd 5vsf
        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 4ft2 4ft4 4fwf 4hon 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

(-) Related Entries Specified in the PDB File

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