Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CATALYTIC DOMAIN OF MUTY FROM ESCHERICHIA COLI K20A MUTANT COMPLEXED TO ADENINE
 
Authors :  K. Hitomi, A. S. Arvai, J. A. Tainer
Date :  25 May 04  (Deposition) - 21 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. C. Manuel, K. Hitomi, A. S. Arvai, P. G. House, A. J. Kurtz, M. L. Dodson, A. K. Mccullough, J. A. Tainer, R. S. Lloyd
Reaction Intermediates In The Catalytic Mechanism Of Escherichia Coli Muty Dna Glycosylase
J. Biol. Chem. V. 279 46930 2004
PubMed-ID: 15326180  |  Reference-DOI: 10.1074/JBC.M403944200
(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 Taxid562
    FragmentCATALYTIC DOMAIN
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymADENINE GLYCOSYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ADE1Ligand/IonADENINE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , VAL A:45 , GLN A:182 , MET A:185 , HOH A:530 , EDO A:1271BINDING SITE FOR RESIDUE ADE A 1428
2AC2SOFTWAREARG A:58 , ASP A:64 , ASN A:67 , ALA A:68 , GLY A:79 , LEU A:80 , HOH A:520BINDING SITE FOR RESIDUE EDO A 1269
3AC3SOFTWAREALA A:150 , SER A:152 , GLU A:169 , THR A:172 , TYR A:219 , HOH A:319BINDING SITE FOR RESIDUE EDO A 1270
4AC4SOFTWAREGLU A:37 , SER A:120 , THR A:121 , ASP A:138 , MET A:185 , HOH A:369 , HOH A:559 , ADE A:1428BINDING SITE FOR RESIDUE EDO A 1271
5AC5SOFTWARECYS A:192 , CYS A:199 , CYS A:202 , GLN A:205 , CYS A:208 , ALA A:211BINDING SITE FOR RESIDUE SF4 A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WEI)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:219 -Pro A:220

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WEI)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ENDONUCLEASE_III_2PS01155 Endonuclease III family signature.MUTY_ECOLI102-131  1A:102-131
2ENDONUCLEASE_III_1PS00764 Endonuclease III iron-sulfur binding region signature.MUTY_ECOLI192-208  1A:192-208

(-) Exons   (0, 0)

(no "Exon" information available for 1WEI)

(-) 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
(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:220
 aligned with MUTY_ECOLI | P17802 from UniProtKB/Swiss-Prot  Length:350

    Alignment length:224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
           MUTY_ECOLI     1 MQASQFSAQVLDWYDKYGRKTLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSEQVTPAVGVERFNQAMMDLGAMICTRSKPKCSLCPLQNGCIAAANNSWALYPGKKP 224
               SCOP domains d1weia_ A: Catalytic domain of MutY                                                                                                                                                                                              SCOP domains
               CATH domains 1weiA01             1weiA02 A:21-132 Hypothetical protein; domain 2                                                                 1weiA01 A:1-20, A:133-224 Helix-h airpin-Helix base-excisi on DNA r epair enzymes (C-termina CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------HHH-1weiA01 A:99-128          ------------------- ----------------- ------------------------ EndIII_4 Fe-2S-1w---------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------HhH-GPD-1weiA02 A:35-170                                                                                                                -------------------- -------- ------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhh......hhhhhhhhhh-........hhhhhhhhh-hhhhhh...hhhhhhhhhhhhhhh-........-.......hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------ENDONUCLEASE_III_2            ------------------------------------------------------------ENDONUCLEASE_III_---------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wei A   1 MQASQFSAQVLDWYDKYGRATLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLAR-YAVSGWPGKKEVENKLW-LSEQVTPAVGVERFNQAMMDLGAM-CTRSKPKC-LCPLQNGCIAAANNSWALYPGKKP 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      |150       160    | |170       180       190 |      |-|      210       220    
                                                                                                                                                                            147 |             165 |                    190 |    199 |                       
                                                                                                                                                                              149               167                      192      201                       

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: HHH (112)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MUTY_ECOLI | P17802)
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ADE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SF4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:219 - Pro A:220   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1wei
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MUTY_ECOLI | P17802
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.2.2.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MUTY_ECOLI | P17802
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MUTY_ECOLI | P178021kg2 1kg3 1kg4 1kg5 1kg6 1kg7 1kqj 1mud 1mun 1muy 1wef 1weg

(-) Related Entries Specified in the PDB File

1wef THE SAME PROTEIN, K20A MUTANT WITHOUT ADENINE
1weg THE SAME PROTEIN WITH DIFFERENT MUTATION K142A