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(-) Description

Title :  MUTY ADENINE GLYCOSYLASE BOUND TO A TRANSITION STATE ANALOG (1N) PAIRED WITH DG IN DUPLEXED DNA
 
Authors :  V. L. O'Shea, M. P. Horvath, S. S. David
Date :  11 Jan 09  (Deposition) - 19 Jan 10  (Release) - 19 Jan 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protein-Dna Complex, Dna Glycosylase, Transition State Analog, Dna Repair, Glycosidase, Hydrolase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. L. O'Shea, S. Cao, J. L. Richards, M. P. Horvath, S. S. David
Structural Illumination Of A Muty Glycosylase Reaction Coordinate Intermediate
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - A/G-SPECIFIC ADENINE GLYCOSYLASE
    ChainsA
    EC Number3.2.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMUTY
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422
 
Molecule 2 - 5'-D(*AP*AP*GP*AP*CP*GP*TP*GP*GP*AP*C)-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 5'-D(*T*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3'
    ChainsC
    EngineeredYES
    Other DetailsDNA CHEMICALLY SYNTHESIZED WITH 1N TRANSITION STATE ANALOG
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NRI1Mod. NucleotidePHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL)ESTER
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:153 , CYS A:198 , CYS A:205 , CYS A:208 , GLN A:211 , CYS A:214 , ALA A:222BINDING SITE FOR RESIDUE SF4 A 400
2AC2SOFTWARESER A:118 , VAL A:123 , HOH A:403 , HOH A:467 , HOH C:450 , HOH C:451BINDING SITE FOR RESIDUE CA A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:225 -Pro A:226
2Glu A:329 -Pro A:330

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3FSP)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:353
 aligned with MUTY_GEOSE | P83847 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:353
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357   
           MUTY_GEOSE     8 FPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKRDSTGLLANLWEFPSCETDGADGKEKLEQMVGEQYGLQVELTEPIVSFEHAFSHLVWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS 360
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3fspA01            3fspA02 A:27-138 Hypothetical protein; domain 2                                                                 3fspA01 A:8-26,A:139-234 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)      3fspA03 A:235-360 Nucleoside Triphosphate Pyrophosphohydrolase                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..hhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhh.hhhhhhhh......hhhhhhhhhhhhhhhhhhh.....hhhhhhh....hhhhhhhhhhhhh.......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh................hhhhhhhhhhhh.........eeeeeeeeeee.....eeee...............eee.....hhhhhhhhh...............eeeee...eeeeeeeeeee..........eeeehhhhhhhh..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fsp A   8 FPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVDGNVMRVLSRLFLVTDDIAKPSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKMKKTAVKQVPLAVAVLADDEGRVLIRKRDSTGLLANLWEFPSCETDGADGKEKLEQMVGEQYGLQVELTEPIVSFEHAFSHLVWQLTVFPGRLVHGGPVEEPYRLAPEDELKAYAFPVSHQRVWREYKEWAS 360
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357   

Chain B from PDB  Type:DNA  Length:11
                                           
                 3fsp B   1 AAGACGTGGAC  11
                                    10 

Chain C from PDB  Type:DNA  Length:10
                                          
                 3fsp C  13 GTCCAxGTCT  22
                                 |  22
                                18-NRI

   Legend:   → Mismatch (orange background)
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  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 3FSP)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MUTY_GEOSE | P83847)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0019104    DNA N-glycosylase activity    Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MUTY_GEOSE | P838471rrq 1rrs 1vrl 3g0q 4yoq 4yph 4ypr 5dpk 5kn8 5kn9

(-) Related Entries Specified in the PDB File

1rrq MUTY BOUND TO DNA WITH AN A:8-OXOG BASEPAIR, THE LESION RECOGNITION COMPLEX
1rrs MUTY BOUND TO DNA WITH AN ABASIC SITE
1vrl MUTY BOUND TO DNA AND ADENINE FREE BASE
3fsq