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(-) Description

Title :  THE 5-HYDROXYMETHYLCYTOSINE-SPECIFIC RESTRICTION ENZYME ABASI IN A COMPLEX WITH PRODUCT-LIKE DNA
 
Authors :  J. R. Horton, X. Cheng
Date :  09 Apr 14  (Deposition) - 25 Jun 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Hydroxymethylcytosine-Dependent Restriction Enzyme, Hydrolase, Vsr Endonuclease-Like, Sra Domain-Like, Epigenetic Sequencing Tool (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Horton, J. G. Borgaro, R. M. Griggs, A. Quimby, S. Guan, X. Zhang, G. G. Wilson, Y. Zheng, Z. Zhu, X. Cheng
Structure Of 5-Hydroxymethylcytosine-Specific Restriction Enzyme, Abasi, In Complex With Dna.
Nucleic Acids Res. V. 42 7947 2014
PubMed-ID: 24895434  |  Reference-DOI: 10.1093/NAR/GKU497
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA 18-MER
    ChainsE, F
    EngineeredYES
    Organism ScientificT4LIKEVIRUS
    Organism Taxid10663
    SyntheticYES
 
Molecule 2 - DNA 14-MER
    ChainsG, H
    EngineeredYES
    Organism ScientificT4LIKEVIRUS
    Organism Taxid10663
    SyntheticYES
 
Molecule 3 - UNCHARACTERIZED PROTEIN ABASI
    ChainsB, A, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid469008
    Expression System VariantBL21(DE3)
    GeneABSDF3356
    MutationYES
    Organism ScientificACINETOBACTER BAUMANNII
    Organism Taxid509170
    StrainSDF

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFGH

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
15HC2Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
2EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU C:247 , TRP C:262 , ARG C:269binding site for residue EDO C 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gln B:129 -Glu B:130
2Arg A:81 -Asn A:82
3Gln A:129 -Glu A:130
4Gly A:265 -Pro A:266
5Leu C:180 -Gly C:181

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PAR)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.......hhhhhhhhhhhhhh......eeeeeee.....eeeeeeee....eeeeee..........eee.........eeehhhhhh.......ee....eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhheee.....ee.hhhhhhhhh..........eee......eeee...........eee.....eeee...hhhhhhhhhhhhhhh..eeeeeeeee......eeeeeeeeeeeee......eeeeeee.eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4par A   5 ASSDLTDYVIRQLGRTKNKRYEAYVVSRIIHLLNDFTLKFVTQQFVRLSNKKIALTDLYFPQLGIHIEVDEGHHFLRNSKMEYSLNQIDEPLYSISQTESDAMREEDIISITGHKIFRVNVFKNQEGQPQNLENIHQQIDKIIEEIKTAKNKLIEASTFKEWNIETEYNPQTYIDLGRISLADNVVLKTTKDVCNCFGYSYKNYQRGGALHPYKKDTLIWFPRLYENKDWINTISPDGLTITEKSTDETITLKKLEEWKNGPQKRIVFARVKDNLSSRAMYRFMGLYEFQKADLKDGAVWKRVKSEVQTYSPKE 318
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314    

Chain B from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.......hhhhhhhhhhhhhh......eeeeeee.....eeeeeeee....eeeeee..........eee.........eeehhhhhh.......ee....eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhheee.hhh.ee.hhhhhhhhh..........eee......eeee.........eeeee.....eeeeee.hhhhhhhhhhhhhhh..eeeeeeeee......eeeeeeeeeeeeee.....eeeeeee.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4par B   5 ASSDLTDYVIRQLGRTKNKRYEAYVVSRIIHLLNDFTLKFVTQQFVRLSNKKIALTDLYFPQLGIHIEVDEGHHFLRNSKMEYSLNQIDEPLYSISQTESDAMREEDIISITGHKIFRVNVFKNQEGQPQNLENIHQQIDKIIEEIKTAKNKLIEASTFKEWNIETEYNPQTYIDLGRISLADNVVLKTTKDVCNCFGYSYKNYQRGGALHPYKKDTLIWFPRLYENKDWINTISPDGLTITEKSTDETITLKKLEEWKNGPQKRIVFARVKDNLSSRAMYRFMGLYEFQKADLKDGAVWKRVKSEVQTYSPK 317
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314   

Chain C from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh.......hhhhhhhhhhhhhh......eeeeeee.....eeeeeeee....eeeeee..........eee.........eeehhhhhh......eee....eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..eee.....ee.hhhhhhhhh..........eee......eeee.........eeeee.....eeeeee.hhhhhhhhhhhhhh...eeeeeeeee......eeeeeeeeeeeeeee...eeeeeeee.eee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4par C   4 KASSDLTDYVIRQLGRTKNKRYEAYVVSRIIHLLNDFTLKFVTQQFVRLSNKKIALTDLYFPQLGIHIEVDEGHHFLRNSKMEYSLNQIDEPLYSISQTESDAMREEDIISITGHKIFRVNVFKNQEGQPQNLENIHQQIDKIIEEIKTAKNKLIEASTFKEWNIETEYNPQTYIDLGRISLADNVVLKTTKDVCNCFGYSYKNYQRGGALHPYKKDTLIWFPRLYENKDWINTISPDGLTITEKSTDETITLKKLEEWKNGPQKRIVFARVKDNLSSRAMYRFMGLYEFQKADLKDGAVWKRVKSEVQTYSPK 317
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313    

Chain D from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh......hhhhhhhhhhhhhh......eeeeeee.....eeeeeeee....eeeeee..........eee.........eee.............ee....eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhhhhheee.hhh.ee.hhhhhhhhh..........eee......eeee.........eeeee.....eeeeee.hhhhhhhhhhhhhhh..eeeeeeeee......eeeeeeeeeeeeeee...eeeeeeee.eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4par D   5 ASSDLTDYVIRQLGRTKNKRYEAYVVSRIIHLLNDFTLKFVTQQFVRLSNKKIALTDLYFPQLGIHIEVDEGHHFLRNSKMEYSLNQIDEPLYSISQTESDAMREEDIISITGHKIFRVNVFKNQEGQPQNLENIHQQIDKIIEEIKTAKNKLIEASTFKEWNIETEYNPQTYIDLGRISLADNVVLKTTKDVCNCFGYSYKNYQRGGALHPYKKDTLIWFPRLYENKDWINTISPDGLTITEKSTDETITLKKLEEWKNGPQKRIVFARVKDNLSSRAMYRFMGLYEFQKADLKDGAVWKRVKSEVQTYSPK 317
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314   

Chain E from PDB  Type:DNA  Length:18
                                                  
                 4par E   1 TGCTxGATACAATAGGCC  18
                                |   10        
                                5-5HC         

Chain F from PDB  Type:DNA  Length:18
                                                  
                 4par F   1 TGCTxGATACAATAGGCC  18
                                |   10        
                                5-5HC         

Chain G from PDB  Type:DNA  Length:14
                                              
                 4par G  29 TATTGTATCGAGCA  42
                                    38    

Chain H from PDB  Type:DNA  Length:14
                                              
                 4par H  29 TATTGTATCGAGCA  42
                                    38    

   Legend:   → Mismatch (orange background)
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    → 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 4PAR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4PAR)

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  Cis Peptide Bonds
    Arg A:81 - Asn A:82   [ RasMol ]  
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    Gln B:129 - Glu B:130   [ RasMol ]  
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    Leu C:180 - Gly C:181   [ RasMol ]  
 

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