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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CORE FRAGMENT OF MUTY FROM E.COLI AT 1.55A RESOLUTION
 
Authors :  R. Gilboa, A. Kilshtein, D. O. Zharkov, J. H. Kycia, S. E. Gerchman, A. P. G. Shoham
Date :  26 Nov 01  (Deposition) - 26 Nov 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Dna Repair, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Gilboa, A. Kilshtein, D. O. Zharkov, J. H. Kycia, S. E. Gerchman, A. P. Grollman, G. Shoham
Analysis Of The E. Coli Muty Dna Glycosylase Structure And Function By Site-Directed Mutagenesis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - A/G-SPECIFIC ADENINE GLYCOSYLASE
    Chains: A
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET13A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN
    Gene: MUTY
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SF41Ligand/IonIRON/SULFUR CLUSTER
3SO43Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:69 , LEU A:70 , HOH A:512 , HOH A:546 , HOH A:557 , HOH A:562BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREGLY A:176 , VAL A:177 , GLU A:178 , ARG A:179 , HOH A:590 , HOH A:622 , HOH A:672BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREGLU A:161 , TRP A:165 , HOH A:527 , HOH A:616 , HOH A:704BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWARECYS A:192 , CYS A:199 , CYS A:202 , CYS A:208BINDING SITE FOR RESIDUE SF4 A 300
5AC5SOFTWAREGLN A:42 , THR A:43 , ARG A:58 , ASP A:64 , GLY A:79 , LEU A:80BINDING SITE FOR RESIDUE GOL A 310
6AC6SOFTWAREPHE A:108 , ARG A:119 , PHE A:134 , ASN A:213 , HOH A:510 , HOH A:535BINDING SITE FOR RESIDUE GOL A 311
7AC7SOFTWAREPRO A:30 , TYR A:31 , THR A:61 , VAL A:62 , LYS A:103 , PHE A:104 , HOH A:518 , HOH A:684BINDING SITE FOR RESIDUE GOL A 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KG3)

(-) 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 1KG3)

(-) 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 1KG3)

(-) 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:224
 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 d1kg3a_ A: Catalytic domain of MutY                                                                                                                                                                                              SCOP domains
               CATH domains 1kg3A01             1kg3A02 A:21-132 Hypothetical protein; domain 2                                                                 1kg3A01 A:1-20,A:133-224 Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)   CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------HHH-1kg3A01 A:99-128          ---------------------------------------------------------------EndIII_4Fe-2S-1kg---------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------HhH-GPD-1kg3A02 A:35-170                                                                                                                ------------------------------------------------------ Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhh....hhhhhhhhhhhhhh......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh......hhhhh.....hhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------ENDONUCLEASE_III_2            ------------------------------------------------------------ENDONUCLEASE_III_---------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kg3 A   1 MQASQFSAQVLDWYDKYGRKTLPWQIDKTPYKVWLSEVMLQQTQVATVIPYFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQVATLHGGKFPETFEEVAALPGVGRSTAGAILSLSLGKHFPILDGNVKRVLARCYAVSGWPGKKEVENKLWSLSEQVTPAVGVERFNQAMMDLGAMICTRSKPKCSLCPLQNGCIAAANNSWALYPGKKP 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   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
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Clan: HHH (112)
(-)
Clan: no clan defined [family: EndIII_4Fe-2S] (10)

(-) 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MUTY_ECOLI | P17802: 1kg2 1kg4 1kg5 1kg6 1kg7 1kqj 1mud 1mun 1muy 1wef 1weg 1wei

(-) Related Entries Specified in the PDB File

1kg2 CRYSTAL STRUCTURE OF THE CORE FRAGMENT OF MUTY FROM E.COLI AT 1.20A RESOLUTION (DIFFERENT CRYSTALLIZATION CONCENTRATION IN COMPARISON TO 1KG3).
1kg4 CRYSTAL STRUCTURE OF THE K142A MUTANT OF E. COLI MUTY (CORE FRAGMENT)
1kg5 CRYSTAL STRUCTURE OF THE K142Q MUTANT OF E.COLI MUTY (CORE FRAGMENT)
1kg6 CRYSTAL STRUCTURE OF THE K142R MUTANT OF E.COLI MUTY (CORE FRAGMENT)
1kg7 CRYSTAL STRUCTURE OF THE E161A MUTANT OF E.COLI MUTY (CORE FRAGMENT)