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(-) Description

Title :  CRYSTAL STRUCTURE OF MVNEI1/THF COMPLEX
 
Authors :  K. Imamura, S. Wallace, S. Doublie
Date :  01 Jul 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Helix Two Turns Helix, Zinc-Less Finger, Hydrolase, Thf, Dna Damage, Dna Repair, Dna-Binding, Glycosidase, Lyase, Multifunctional Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Imamura, S. S. Wallace, S. Doublie
Structural Characterization Of A Viral Neil1 Ortholog Unliganded And Bound To Abasic Site-Containing Dna
J. Biol. Chem. V. 284 26174 2009
PubMed-ID: 19625256  |  Reference-DOI: 10.1074/JBC.M109.021907

(-) Compounds

Molecule 1 - FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
    ChainsA, B
    EC Number3.2.2.23
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainROSETTA(DE3)PLYS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneL315
    Organism CommonAPMV
    Organism ScientificACANTHAMOEBA POLYPHAGA MIMIVIRUS
    Organism Taxid212035
    SynonymFAPY-DNA GLYCOSYLASE, DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE, AP LYASE, ENDONUCLEASE VIII, MVNEI1
 
Molecule 2 - DNA
    ChainsC, E
    EngineeredYES
    Other DetailsNUCLEOTIDE SYNTHESIS
    SyntheticYES
 
Molecule 3 - DNA
    ChainsD, F
    EngineeredYES
    Other DetailsNUCLEOTIDE SYNTHESIS
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)A CD  
Biological Unit 2 (1x) B  EF

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
13DR2Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:274 , ARG A:277 , HOH A:2017 , DC C:6 , DG D:21 , HOH D:2070BINDING SITE FOR RESIDUE GOL A 3545

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A46)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:48 -Pro A:49
2Leu B:48 -Pro B:49

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A46)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FPG_CATPS51068 Formamidopyrimidine-DNA glycosylase catalytic domain profile.FPG_MIMIV2-117
 
  2A:2-117
B:2-117
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FPG_CATPS51068 Formamidopyrimidine-DNA glycosylase catalytic domain profile.FPG_MIMIV2-117
 
  1A:2-117
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FPG_CATPS51068 Formamidopyrimidine-DNA glycosylase catalytic domain profile.FPG_MIMIV2-117
 
  1-
B:2-117

(-) Exons   (0, 0)

(no "Exon" information available for 3A46)

(-) 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:288
 aligned with FPG_MIMIV | Q5UQ00 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:288
                                                                                                                                                                                                                                                                                                                       287  
                                    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     |  
            FPG_MIMIV     2 PEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQK--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..eeeeeee..hhhhhh...hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeeeeeeee....eeee......eeeeeee....eeeeee.....eeeee.hhhhhhhhhh............hhhhhhhh..hhhhhhhh........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..................................eee...........eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE FPG_CAT  PDB: A:2-117 UniProt: 2-117                                                                                ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a46 A   2 PEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQKLE 289
                                    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        

Chain B from PDB  Type:PROTEIN  Length:288
 aligned with FPG_MIMIV | Q5UQ00 from UniProtKB/Swiss-Prot  Length:287

    Alignment length:288
                                                                                                                                                                                                                                                                                                                       287  
                                    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     |  
            FPG_MIMIV     2 PEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQK--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..eeeeeee..hhhhh....hhhhhhhh..eeeeeeeee..eeeeeeee..eeeeeeeeeee....eeee......eeeeeee....eeeeee.....eeeee.hhhhhhhhhh............hhhhhhhh..hhhhhhhh........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh................................eee...........eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE FPG_CAT  PDB: B:2-117 UniProt: 2-117                                                                                ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3a46 B   2 PEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTGMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQKLE 289
                                    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        

Chain C from PDB  Type:DNA  Length:13
                                             
                 3a46 C   1 GTAGACCTGGACG  13
                                    10   

Chain D from PDB  Type:DNA  Length:13
                                             
                 3a46 D  14 CGTCCAxGTCTAC  26
                                  | 23   
                                 20-3DR  

Chain E from PDB  Type:DNA  Length:13
                                             
                 3a46 E   1 GTAGACCTGGACG  13
                                    10   

Chain F from PDB  Type:DNA  Length:13
                                             
                 3a46 F  14 CGTCCAxGTCTAC  26
                                  | 23   
                                 20-3DR  

   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 3A46)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3A46)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A46)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FPG_MIMIV | Q5UQ00)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003906    DNA-(apurinic or apyrimidinic site) lyase activity    Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
    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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008534    oxidized purine nucleobase lesion DNA N-glycosylase activity    Catalysis of the removal of oxidized purine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar. The reaction involves the formation of a covalent enzyme-substrate intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apurinic (AP) site.
    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:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).

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 Related Entries

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

UniProtKB/Swiss-Prot
        FPG_MIMIV | Q5UQ003a42 3a45 3vk7 3vk8 4nrw

(-) Related Entries Specified in the PDB File

3a42 MVNEI1 APO FORM 1
3a45 MVNEI1 APO FORM 2