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(-) Description

Title :  STRUCTURE OF THE C-TERMINAL DOMAIN OF BACILLUS SUBTILIS MUTL BOUND TO ZN2+
 
Authors :  A. Guarne, M. C. Pillon
Date :  23 Oct 09  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.26
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mismatch Repair, Mutl, Endonuclease, Zn-Binding Protein, Dna Damage, Dna Repair, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Pillon, J. J. Lorenowicz, M. Uckelmann, A. D. Klocko, R. R. Mitchell, Y. S. Chung, P. Modrich, G. C. Walker, L. A. Simmons, P. Friedhoff, A. Guarne
Structure Of The Endonuclease Domain Of Mutl: Unlicensed To Cut.
Mol. Cell V. 39 145 2010
PubMed-ID: 20603082  |  Reference-DOI: 10.1016/J.MOLCEL.2010.06.027

(-) Compounds

Molecule 1 - DNA MISMATCH REPAIR PROTEIN MUTL
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX-HTA
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PPROEX-HTA
    Fragment: RESIDUES 434-627
    Gene: BSU17050, MUTL
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:468 , CYS A:604 , HIS A:606 , ARG A:608 , HOH A:628BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREHIS A:464 , GLU A:468 , CYS A:573BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWAREHOH B:53 , GLU B:468 , CYS B:604 , HIS B:606BINDING SITE FOR RESIDUE ZN B 3
4AC4SOFTWAREHOH B:2 , HIS B:464 , GLU B:468 , CYS B:573BINDING SITE FOR RESIDUE ZN B 4

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KDK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KDK)

(-) 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:186
 aligned with MUTL_BACSU | P49850 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:192
                                   442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622  
           MUTL_BACSU   433 SDRVPIMYPIGQMHGTYILAQNENGLYIIDQHAAQERIKYEYFREKVGEVEPEVQEMIVPLTFHYSTNEALIIEQHKQELESVGVFLESFGSNSYIVRCHPAWFPKGEEAELIEEIIQQVLDSKNIDIKKLREEAAIMMSCKGSIKANRHLRNDEIKALLDDLRSTSDPFTCPHGRPIIIHHSTYEMEKMFK 624
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeee...eeeeee..eeeeeehhhhhhhhhhhhhhhhh......eeeeeeeeeee...hhhhhhhhh.hhhhhh....ee....eeeeeeee......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.------...hhhhhhhhhhhhhh.............eeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kdk A 433 MDRVPIMYPIGQMHGTYILAQNENGLYIIDQHAAQERIKYEYFREKVGEVEPEVQEMIVPLTFHYSTNEALIIEQHKQELESVGVFLESFGSNSYIVRCHPAWFPKGEEAELIEEIIQQVLDSKNIDIKKLREEAAIMMSCK------RHLRNDEIKALLDDLRSTSDPFTCPHGRPIIIHHSTYEMEKMFK 624
                                   442       452       462       472       482       492       502       512       522       532       542       552       562       572 |     582       592       602       612       622  
                                                                                                                                                                       574    581                                           


Chain B from PDB  Type:PROTEIN  Length:184
 aligned with MUTL_BACSU | P49850 from UniProtKB/Swiss-Prot  Length:627

    Alignment length:190
                                   444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624
           MUTL_BACSU   435 RVPIMYPIGQMHGTYILAQNENGLYIIDQHAAQERIKYEYFREKVGEVEPEVQEMIVPLTFHYSTNEALIIEQHKQELESVGVFLESFGSNSYIVRCHPAWFPKGEEAELIEEIIQQVLDSKNIDIKKLREEAAIMMSCKGSIKANRHLRNDEIKALLDDLRSTSDPFTCPHGRPIIIHHSTYEMEKMFK 624
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --MutL_C-3kdkB01 B:437-583                                                                                                                           ----------------------------------------- Pfam domains (1)
           Pfam domains (2) --MutL_C-3kdkB02 B:437-583                                                                                                                           ----------------------------------------- Pfam domains (2)
         Sec.struct. author .....eeeeee...eeeeee..eeeeeehhhhhhhhhhhhhhhhh......eeeeeeeeeee.hhhhhhhhhhhhhhhhhh...eee....eeeeeeee......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.------...hhhhhhhhhhhhhh.............eeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kdk B 435 RVPIMYPIGQMHGTYILAQNENGLYIIDQHAAQERIKYEYFREKVGEVEPEVQEMIVPLTFHYSTNEALIIEQHKQELESVGVFLESFGSNSYIVRCHPAWFPKGEEAELIEEIIQQVLDSKNIDIKKLREEAAIMMSCK------RHLRNDEIKALLDDLRSTSDPFTCPHGRPIIIHHSTYEMEKMFK 624
                                   444       454       464       474       484       494       504       514       524       534       544       554       564       574      |584       594       604       614       624
                                                                                                                                                                     574    581
   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 3KDK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KDK)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: MutL_C] (4)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MUTL_BACSU | P49850)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0030983    mismatched DNA binding    Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
    GO:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
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: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:0006298    mismatch repair    A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.
cellular component
    GO:0032300    mismatch repair complex    Any complex formed of proteins that act in mismatch repair.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MUTL_BACSU | P49850: 3gab 3kdg

(-) Related Entries Specified in the PDB File

3gab C-TERMINAL DOMAIN OF BACILLUS SUBTILIS MUTL CRYSTAL FORM I
3kdg C-TERMINAL DOMAIN OF BACILLUS SUBTILIS MUTL CRYSTAL FORM II