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(-) Description

Title :  CRYSTAL STRUCTURE OF D144N MUTY BOUND TO ITS ANTI-SUBSTRATE
 
Authors :  L. Wang, S. Lee, G. L. Verdine
Date :  13 Mar 15  (Deposition) - 27 May 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.59
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,D  (1x)
Biol. Unit 2:  B,E,F  (1x)
Keywords :  8-Oxoguanine, Base-Excision Repair, Anti-Substrate, Hydrolase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Wang, S. J. Lee, G. L. Verdine
Structural Basis For Avoidance Of Promutagenic Dna Repair B Muty Adenine Dna Glycosylase.
J. Biol. Chem. V. 290 17096 2015
PubMed-ID: 25995449  |  Reference-DOI: 10.1074/JBC.M115.657866

(-) Compounds

Molecule 1 - A/G-SPECIFIC ADENINE GLYCOSYLASE
    Chains: A, B
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: GEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid: 1422
 
Molecule 2 - DNA (5'-D(*T*GP*TP*CP*CP*AP*CP*GP*TP*CP*T)-3')
    Chains: C, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')
    Chains: D, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
18OG2Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
18OG1Mod. Nucleotide8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE
2SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:198 , CYS A:205 , CYS A:208 , CYS A:214 , ALA A:222binding site for residue SF4 A 400
2AC2SOFTWARECYS B:198 , CYS B:205 , CYS B:208 , CYS B:214binding site for residue SF4 B 400
3AC3SOFTWAREGLN A:48 , THR A:49 , LEU A:86 , GLY A:87 , TYR A:88 , TYR A:89 , GLY A:260 , LEU A:261 , LEU A:262 , PHE A:307 , SER A:308 , HIS A:309 , DA C:17 , DG C:19 , DA D:4 , DT D:7binding site for Di-nucleotide DC D 5 and 8OG D 6
4AC4SOFTWAREGLN A:48 , THR A:49 , GLY A:85 , LEU A:86 , GLY A:87 , TYR A:88 , TYR A:89 , LEU A:261 , LEU A:262 , HIS A:305 , ALA A:306 , PHE A:307 , SER A:308 , PRO A:345 , VAL A:346 , DA C:17 , DC D:5 , DG D:8binding site for Di-nucleotide 8OG D 6 and DT D 7
5AC5SOFTWAREGLN B:48 , THR B:49 , LEU B:86 , GLY B:87 , TYR B:88 , TYR B:89 , GLY B:260 , LEU B:261 , LEU B:262 , PHE B:307 , SER B:308 , HIS B:309 , DA E:17 , DG E:19 , DA F:4 , DT F:7 , HOH F:101binding site for Di-nucleotide DC F 5 and 8OG F 6
6AC6SOFTWAREGLN B:48 , THR B:49 , GLY B:85 , LEU B:86 , GLY B:87 , TYR B:88 , TYR B:89 , LEU B:261 , LEU B:262 , HIS B:305 , ALA B:306 , PHE B:307 , SER B:308 , PRO B:345 , VAL B:346 , DA E:17 , DC F:5 , DG F:8 , HOH F:101binding site for Di-nucleotide 8OG F 6 and DT F 7

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:225 -Pro A:226
2Leu B:225 -Pro B:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YPR)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhh.hhhhh..........eeeeeeeeee....eeeeee..........ee..ee......hhhhhhh........eeee....eeeeeee..eeeeeeeeeeeee........eeeee.hhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ypr A   6 ERFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVNGNVMRVLSRLFLVTDDIAKCSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKRDSTGLLANLWEFPSCETDGADGKEKLEQMVGEQYGLQVELTEPIVSFEHAFSHLVWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS 360
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355     


Chain B from PDB  Type:PROTEIN  Length:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh......hhhhhhhh...hhhhhhhhhhhhhh......hhhhhhhhhhhhh........hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh.hhhhhhhhhh.hhhhh.........eeeeeeeeeee....eeeeee..........ee..eee.....hhhhhhhh..........eeeeee...eeeeeeeeeee..........eeeee.hhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ypr B   6 ERFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVNGNVMRVLSRLFLVTDDIAKCSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKRDSTGLLANLWEFPSCETDGADGKEKLEQMVGQVELTEPIVSFEHAFSHLVWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS 360
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285 ||    300       310       320       330       340       350       360
                                                                                                                                                                                                                                                                                                                   287|                                                                   
                                                                                                                                                                                                                                                                                                                    293                                                                   


Chain C from PDB  Type:DNA  Length:10
                                          
                 4ypr C  13 GTCCACGTCT  22
                                    22


Chain D from PDB  Type:DNA  Length:11
                                           
                 4ypr D   1 AAGACxTGGAC  11
                                 |  10 
                                 6-8OG 


Chain E from PDB  Type:DNA  Length:10
                                          
                 4ypr E  13 GTCCACGTCT  22
                                    22


Chain F from PDB  Type:DNA  Length:11
                                           
                 4ypr F   1 AAGACxTGGAC  11
                                 |  10 
                                 6-8OG
   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 4YPR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)

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  MUTY_GEOSE | P83847
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  3.2.2.-
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 Related Entries

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UniProtKB/Swiss-Prot
        MUTY_GEOSE | P83847: 1rrq 1rrs 1vrl 3fsp 3g0q 4yoq 4yph 5dpk 5kn8 5kn9

(-) Related Entries Specified in the PDB File

4yoq 4yph