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(-) Description

Title :  CRYSTAL STRUCTURE OF SPODOPTERA FRUGIPERDA DNMT2 E260A/E261A/K263A MUTANT
 
Authors :  S. Li, J. Du, H. Yang, J. Yin, J. Zhong, J. Ding
Date :  09 Sep 12  (Deposition) - 14 Nov 12  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.71
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Sah Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Li, J. Du, H. Yang, J. Yin, J. Ding, J. Zhong
Functional And Structural Characterization Of Dnmt2 From Spodoptera Frugiperda.
J Mol Cell Biol V. 5 64 2013
PubMed-ID: 23103599  |  Reference-DOI: 10.1093/JMCB/MJS057

(-) Compounds

Molecule 1 - DNMT2
    Chains: A, B, C, D
    EC Number: 2.1.1.-
    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
    Gene: DNMT2
    Mutation: YES
    Organism Common: FALL ARMYWORM
    Organism Scientific: SPODOPTERA FRUGIPERDA
    Organism Taxid: 7108
    Strain: SF9
    Synonym: DNA METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:9 , SER A:10 , GLY A:11 , ILE A:12 , GLY A:14 , ASP A:33 , ILE A:34 , ASN A:35 , ARG A:54 , ASN A:55 , ILE A:56 , SER A:75 , PRO A:77 , SER A:97 , ASN A:316 , SER A:317 , VAL A:318BINDING SITE FOR RESIDUE SAH A 401
2AC2SOFTWAREGLY A:103 , ASP A:106 , ASP B:133 , GLU B:137BINDING SITE FOR RESIDUE CA A 402
3AC3SOFTWARETYR B:9 , SER B:10 , GLY B:11 , ILE B:12 , GLY B:13 , GLY B:14 , ASP B:33 , ILE B:34 , ASN B:35 , ASN B:55 , ILE B:56 , SER B:75 , PRO B:77 , GLN B:79 , SER B:97 , ASN B:316 , SER B:317BINDING SITE FOR RESIDUE SAH B 401
4AC4SOFTWAREASP A:133 , GLU A:137 , GLY B:103 , ASP B:106 , GLN B:107BINDING SITE FOR RESIDUE CA B 402
5AC5SOFTWARETYR C:9 , SER C:10 , GLY C:11 , ILE C:12 , ASP C:33 , ILE C:34 , ARG C:54 , ASN C:55 , ILE C:56 , SER C:75 , PRO C:77 , SER C:97 , ASN C:316 , SER C:317 , VAL C:318BINDING SITE FOR RESIDUE SAH C 401
6AC6SOFTWAREGLY C:103 , ASP C:106BINDING SITE FOR RESIDUE CA C 402
7AC7SOFTWARETYR D:9 , SER D:10 , GLY D:11 , ILE D:12 , GLY D:14 , ASP D:33 , ILE D:34 , ASN D:35 , ASN D:55 , ILE D:56 , SER D:75 , PRO D:77 , GLN D:79 , SER D:97 , ASN D:316 , SER D:317 , VAL D:318BINDING SITE FOR RESIDUE SAH D 401
8AC8SOFTWAREGLY D:103 , ASP D:106BINDING SITE FOR RESIDUE CA D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H0N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H0N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H0N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H0N)

(-) Exons   (0, 0)

(no "Exon" information available for 4H0N)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4h0na_ A: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh....ee..hhhhhhhhhhhhh...eeee.......ee..ee.........hhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeeeeeee............eeeeeeee...................................hhhhh.hhhhhhhhhhh.ee.......................ee...hhhhhhhhhhhhhhh...hhhhhhhhhh......hhhhhhhhh............hhhhhhhhhhh..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0n A   2 SHKILELYSGIGGMHCAWKESGLDGEIVAAVDINTVANSVYKHNFPETNLLNRNIQQLTPQVIKKWNVDTILMSPPCQPFTRNGKYLDDNDPRTNSFLYLIGILDQLDNVDYILMENVKGFENSTVRNLFIDKLKECNFIYQEFLLCPSTVGVPNSRLRYYCTARRNNLTWPFKRRDEIITRLPKDFGVPHSLESIIEEDVDEKFLVPEKMLRCAKVFDICYKTSKRSCCFTKAYTHYADGTGSIFTDKPREVVQKCYAAAAQNEIGGEKFVELFKELKLRYFTPKEVLMIMCFPKSYNLPTNISMKQCYRLLGNSVNVKVISELLKILFE 332
                                    11        21        31        41        51        61        71        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 


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4h0nb_ B: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh....ee..hhhhhhhhhhhhh...eeee......................hhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeeeeeeehhhhh.......eeeeeeee...................................hhhhh.hhhhhhhhhhh.ee.......................ee...hhhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhh............hhhhhhhhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0n B   2 SHKILELYSGIGGMHCAWKESGLDGEIVAAVDINTVANSVYKHNFPETNLLNRNIQQLTPQVIKKWNVDTILMSPPCQPFTRNGKYLDDNDPRTNSFLYLIGILDQLDNVDYILMENVKGFENSTVRNLFIDKLKECNFIYQEFLLCPSTVGVPNSRLRYYCTARRNNLTWPFKRRDEIITRLPKDFGVPHSLESIIEEDVDEKFLVPEKMLRCAKVFDICYKTSKRSCCFTKAYTHYADGTGSIFTDKPREVVQKCYAAAAQNEIGGEKFVELFKELKLRYFTPKEVLMIMCFPKSYNLPTNISMKQCYRLLGNSVNVKVISELLKILFE 332
                                    11        21        31        41        51        61        71        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 


Chain C from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4h0nc_ C: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh....ee..hhhhhhhhhhhhh...eeee.......ee..ee.........hhhhhhhhhhhh....eeeeeee.hhhhhhhhhhhhhhhhhh.eeeeeeeehhhhhh......eeeeeeee...................................hhhhh.hhhhhhhhhhh.ee.......................ee...hhhhhhhhhhhhh.....hhhhhhhhhh...ee.hhhhhhhhh............hhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0n C   2 SHKILELYSGIGGMHCAWKESGLDGEIVAAVDINTVANSVYKHNFPETNLLNRNIQQLTPQVIKKWNVDTILMSPPCQPFTRNGKYLDDNDPRTNSFLYLIGILDQLDNVDYILMENVKGFENSTVRNLFIDKLKECNFIYQEFLLCPSTVGVPNSRLRYYCTARRNNLTWPFKRRDEIITRLPKDFGVPHSLESIIEEDVDEKFLVPEKMLRCAKVFDICYKTSKRSCCFTKAYTHYADGTGSIFTDKPREVVQKCYAAAAQNEIGGEKFVELFKELKLRYFTPKEVLMIMCFPKSYNLPTNISMKQCYRLLGNSVNVKVISELLKILFE 332
                                    11        21        31        41        51        61        71        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 


Chain D from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4h0nd_ D: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh....ee..hhhhhhhhhhhhh...eeee.......ee..ee.........hhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhhh.eeeeeeeehhhhh.......eeeeeeee...................................hhhhh.hhhhhhhhhhh.ee.......................ee...hhhhhhhhhhhhh.....hhhhhhhhhh......hhhhhhhhh............hhhhhhhhhhhh.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h0n D   2 SHKILELYSGIGGMHCAWKESGLDGEIVAAVDINTVANSVYKHNFPETNLLNRNIQQLTPQVIKKWNVDTILMSPPCQPFTRNGKYLDDNDPRTNSFLYLIGILDQLDNVDYILMENVKGFENSTVRNLFIDKLKECNFIYQEFLLCPSTVGVPNSRLRYYCTARRNNLTWPFKRRDEIITRLPKDFGVPHSLESIIEEDVDEKFLVPEKMLRCAKVFDICYKTSKRSCCFTKAYTHYADGTGSIFTDKPREVVQKCYAAAAQNEIGGEKFVELFKELKLRYFTPKEVLMIMCFPKSYNLPTNISMKQCYRLLGNSVNVKVISELLKILFE 332
                                    11        21        31        41        51        61        71        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
   Legend:   → Mismatch (orange background)
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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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H0N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H0N)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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