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(-) Description

Title :  MVNEI1-G86D
 
Authors :  A. Prakash, S. Doublie
Date :  27 Nov 13  (Deposition) - 01 Jan 14  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  Zinc-Less Finger Domain, Dna Glycosylase, Helix Two-Turns Helix Motif, Thf, Dna Lyase, Hydrolase, Lyase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Prakash, B. L. Carroll, J. B. Sweasy, S. S. Wallace, S. Doublie
Genome And Cancer Single Nucleotide Polymorphisms Of The Human Neil1 Dna Glycosylase: Activity, Structure, And The Effect Of Editing.
Dna Repair V. 14 17 2014
PubMed-ID: 24382305  |  Reference-DOI: 10.1016/J.DNAREP.2013.12.003

(-) Compounds

Molecule 1 - FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
    Chains: A, B
    EC Number: 3.2.2.23, 4.2.99.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ENDONUCLEASE VIII (NEI) 1, MIMI_L315
    Mutation: YES
    Organism Common: APMV
    Organism Scientific: ACANTHAMOEBA POLYPHAGA MIMIVIRUS
    Organism Taxid: 212035
    Synonym: NEI1 (MVNEI1) DNA GLYCOSYLASE, FAPY-DNA GLYCOSYLASE, DNA- (APURINIC OR APYRIMIDINIC SITE) LYASE, AP LYASE
 
Molecule 2 - 5'-D(*GP*TP*AP*GP*AP*CP*CP*TP*GP*GP*AP*CP*G)-3'
    Chains: C, E
    Engineered: YES
    Other Details: COMPLEMENTARY DNA STRAND
    Synthetic: YES
 
Molecule 3 - 5'-D(*CP*GP*TP*CP*CP*AP*(3DR)P*GP*TP*CP*TP*AP*C)-3'
    Chains: D, F
    Engineered: YES
    Other Details: FURAN-CONTAINING DNA STRAND
    Synthetic: YES

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
13DR2Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4NRW)

(-) SS Bonds  (0, 0)

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

(-) 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 4NRW)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NRW)

(-) 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:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..eeeeee...hhhhh....hhhhhhh...eeeeeeee...eeeeeee........eeeeee....eeee......eeeeeee....eeeeee.....eeeee.hhhhhhhhhhh...........hhhhhhhh..hhhhhhhh........hhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh..................................eee...........eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nrw A   2 PEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTDMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQ 286
                                    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:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..eeeeeee..hhhhh....hhhhhh....eeeeeeeee..eeeeeeee..eeeeeeeeeee....eeee......eeeeeee...eeeeeee.....eeeee.hhhhhhhhhhh...........hhhhhhhh..hhhhhhhh........hhhhhhhhhhhh......hhhhh.hhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..................................eee...........eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nrw B   2 PEGPEVALTADILEKYFKGKTLEYIDFISGRYSKSEPEGYDDFIANLPLKVSNVDTKGKFLWFELFDPNDKSNKWYIWNTFGLTDMWSLFEAKYTRAVLSFDNELMAYFSDMRNFGTFKFSNSEKELKRKLNELGPDFLKNDDIDISKIKKYKQPIVALLMDQKKIGSGLGNYLVAEILYRAKIDPHKLGSNLTDQEIENLWYWIKYETKLAYDSNHIGYMVNLENESSKIGRKNYHPNIHPTEKEFDFLVYRKKKDPNGNKVIADKIIGSGKNKRTTYWAPAIQ 286
                                    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
                                             
                 4nrw C   1 GTAGACCTGGACG  13
                                    10   


Chain D from PDB  Type:DNA  Length:13
                                             
                 4nrw D  14 CGTCCAxGTCTAC  26
                                  | 23   
                                 20-3DR  


Chain E from PDB  Type:DNA  Length:13
                                             
                 4nrw E   1 GTAGACCTGGACG  13
                                    10   


Chain F from PDB  Type:DNA  Length:13
                                             
                 4nrw 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 4NRW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

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  Cis Peptide Bonds
    Leu A:48 - Pro A:49   [ RasMol ]  
    Leu B:48 - Pro B:49   [ RasMol ]  
 
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        FPG_MIMIV | Q5UQ00: 3a42 3a45 3a46 3vk7 3vk8

(-) Related Entries Specified in the PDB File

4nrv