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(-) Description

Title :  CRYSTAL STRUCTURE OF APRATAXIN ORTHOLOG HNT3 IN COMPLEX WITH DNA
 
Authors :  Y. Gong, D. Zhu, J. Ding, C. Dou, X. Ren, T. Jiang, D. Wang
Date :  01 Jul 11  (Deposition) - 12 Oct 11  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.91
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Hit Domain, Zinc Finger, Dna Deadenylase, Dna Binding, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Gong, D. Zhu, J. Ding, C. Dou, X. Ren, L. Gu, T. Jiang, D. Wang
Crystal Structures Of Aprataxin Ortholog Hnt3 Reveal The Mechanism For Reversal Of 5'-Adenylated Dna
Nat. Struct. Mol. Biol. V. 18 1297 2011
PubMed-ID: 21984208  |  Reference-DOI: 10.1038/NSMB.2145

(-) Compounds

Molecule 1 - APRATAXIN-LIKE PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 33-232
    Gene: HNT3, SPCC18.09C
    Mutation: YES
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 284812
    Strain: ATCC 38366 / 972
    Synonym: HNT3 PROTEIN, HIT FAMILY PROTEIN 3
 
Molecule 2 - DNA (5'-D(*TP*AP*TP*TP*CP*CP*GP*AP*TP*AP*GP*TP*GP*AP*C)- 3')
    Chains: E, G
    Engineered: YES
    Other Details: SHORT STRAND OF DOUBLE-STRANDED DNA
    Other Details - Source: DNA OLIGONUCLEOTIDES WERE SYNTHESIZED FROM SHANGHAI SANGON BIOTECHNOLOGY COMPANY (SHANGHAI, CHINA).
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*GP*TP*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*GP*AP*G)-3')
    Chains: F, H
    Engineered: YES
    Other Details: LONG STRAND OF DOUBLE-STRANDED DNA
    Other Details - Source: DNA OLIGONUCLEOTIDES WERE SYNTHESIZED FROM SHANGHAI SANGON BIOTECHNOLOGY COMPANY (SHANGHAI, CHINA)
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1SO416Ligand/IonSULFATE ION
2ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:200 , CYS A:203 , HIS A:217 , GLU A:221BINDING SITE FOR RESIDUE ZN A 601
02AC2SOFTWAREARG A:202 , TRP A:225 , LYS A:228 , HOH A:485 , HIS D:83 , HOH D:498BINDING SITE FOR RESIDUE SO4 A 701
03AC3SOFTWAREHIS A:85 , GLY A:140 , ARG A:187 , GLY A:188 , HOH A:272 , LYS B:199BINDING SITE FOR RESIDUE SO4 A 702
04AC4SOFTWAREHIS A:93 , SER A:95 , LEU A:96 , HOH A:267 , HOH A:1000BINDING SITE FOR RESIDUE SO4 A 703
05AC5SOFTWARESER A:121 , GLN A:122 , GLN A:123 , HOH A:245 , HOH A:265 , HOH A:771 , HOH A:1034 , HOH A:1072BINDING SITE FOR RESIDUE SO4 A 704
06AC6SOFTWARECYS B:200 , CYS B:203 , HIS B:217 , GLU B:221BINDING SITE FOR RESIDUE ZN B 601
07AC7SOFTWAREHIS A:83 , HOH A:764 , ARG B:202 , TRP B:225 , LYS B:228BINDING SITE FOR RESIDUE SO4 B 701
08AC8SOFTWAREHIS B:85 , GLY B:140 , ARG B:187 , GLY B:188 , HOH B:257 , LYS C:199BINDING SITE FOR RESIDUE SO4 B 702
09AC9SOFTWAREHIS B:93 , SER B:95 , LEU B:96 , HOH B:270 , HOH B:272BINDING SITE FOR RESIDUE SO4 B 703
10BC1SOFTWAREHOH B:1 , SER B:121 , GLN B:122 , GLN B:123 , HOH B:271 , HOH B:811 , HOH C:290BINDING SITE FOR RESIDUE SO4 B 704
11BC2SOFTWARECYS C:200 , CYS C:203 , HIS C:217 , GLU C:221BINDING SITE FOR RESIDUE ZN C 601
12BC3SOFTWAREHIS B:83 , ARG C:202 , TRP C:225 , LYS C:228BINDING SITE FOR RESIDUE SO4 C 701
13BC4SOFTWAREHIS C:85 , GLY C:140 , ARG C:187 , HOH C:1010 , LYS D:199BINDING SITE FOR RESIDUE SO4 C 702
14BC5SOFTWARELEU C:81 , HIS C:93 , SER C:95 , LEU C:96 , HOH C:256 , HOH C:261 , HOH C:1091 , HOH C:1092BINDING SITE FOR RESIDUE SO4 C 703
15BC6SOFTWAREHOH B:262 , SER C:121 , GLN C:122 , GLN C:123 , HOH C:341 , HOH C:961 , HOH C:1044BINDING SITE FOR RESIDUE SO4 C 704
16BC7SOFTWARECYS D:200 , CYS D:203 , HIS D:217 , GLU D:221BINDING SITE FOR RESIDUE ZN D 601
17BC8SOFTWAREHIS C:83 , ARG D:202 , TRP D:225 , LYS D:228 , HOH D:360 , HOH D:829BINDING SITE FOR RESIDUE SO4 D 701
18BC9SOFTWARELYS A:199 , HIS D:85 , GLY D:140 , ARG D:187 , HOH D:266BINDING SITE FOR RESIDUE SO4 D 702
19CC1SOFTWARELEU D:81 , HIS D:93 , SER D:95 , LEU D:96 , HOH D:246 , HOH D:292BINDING SITE FOR RESIDUE SO4 D 703
20CC2SOFTWARESER D:121 , GLN D:122 , GLN D:123 , HOH D:272 , HOH D:291 , HOH D:809 , HOH D:1018BINDING SITE FOR RESIDUE SO4 D 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3SPD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3SPD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3SPD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3SPD)

(-) Exons   (0, 0)

(no "Exon" information available for 3SPD)

(-) 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:200
 aligned with APTX_SCHPO | O74859 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:200
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
           APTX_SCHPO    33 SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALCNYIKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM 232
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeee...eeeee........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhh.eeeeee.........eeeee.........hhhhhhhhhh..eee...hhhhh.....hhhhhhh.ee......eee.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3spd A  33 SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALANYIKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM 232
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232


Chain B from PDB  Type:PROTEIN  Length:200
 aligned with APTX_SCHPO | O74859 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:200
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
           APTX_SCHPO    33 SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALCNYIKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM 232
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeee...eeeee........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhh.eeeeee.........eeeee.........hhhhhhhhhh..eee...hhhhh.....hhhhhhh.ee......eee.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3spd B  33 SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALANYIKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM 232
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232


Chain C from PDB  Type:PROTEIN  Length:200
 aligned with APTX_SCHPO | O74859 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:200
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
           APTX_SCHPO    33 SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALCNYIKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM 232
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeee...eeeee........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhh.eeeeee.........eeeee.........hhhhhhhhhh..eee...hhhhh.....hhhhhhh.ee......eee.hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3spd C  33 SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALANYIKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM 232
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232


Chain D from PDB  Type:PROTEIN  Length:200
 aligned with APTX_SCHPO | O74859 from UniProtKB/Swiss-Prot  Length:232

    Alignment length:200
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232
           APTX_SCHPO    33 SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALCNYIKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM 232
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeee...eeeee........eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh....hhhhhhh.eeeeee.........eeeee.........hhhhhhhhhh..eee...hhhhh.....hhhhhhh.ee......eee.hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3spd D  33 SFRDNLKVYIESPESYKNVIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKLVSYVQGDLSGLIFDEARNCLSQQLTNEALANYIKVGFHAGPSMNNLHLHIMTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKCWRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM 232
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232


Chain E from PDB  Type:DNA  Length:14
                                              
                 3spd E   1 TATTCCGATAGTGA  14
                                    10    


Chain F from PDB  Type:DNA  Length:14
                                              
                 3spd F   1 GTCACTATCGGAAT  14
                                    10    


Chain G from PDB  Type:DNA  Length:14
                                              
                 3spd G   1 TATTCCGATAGTGA  14
                                    10    


Chain H from PDB  Type:DNA  Length:14
                                              
                 3spd H   1 GTCACTATCGGAAT  14
                                    10
   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 3SPD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3SPD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3SPD)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (APTX_SCHPO | O74859)
molecular function
    GO:0033699    DNA 5'-adenosine monophosphate hydrolase activity    Catalysis of the reaction: 5'-AMP-DNA + H2O = AMP + DNA; nucleophilic release of a covalently linked adenylate residue from a DNA strand, leaving a 5' phosphate terminus.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0030983    mismatched DNA binding    Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
    GO:1990165    single-strand break-containing DNA binding    Interacting selectively and non-covalently with damaged DNA containing single-strand breaks (SSBs).
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  APTX_SCHPO | O74859
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 Related Entries

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

UniProtKB/Swiss-Prot
        APTX_SCHPO | O74859: 3sp4 3spl 3szq 4xba 4ykl

(-) Related Entries Specified in the PDB File

3sp4 THE NATIVE HNT3 IN FREE STATE
3spl THE HNT3 IN COMPLEX WITH DNA AND AMP