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(-)Asym./Biol. Unit
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Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  NGOL
 
Authors :  S. Namadurai, D. Jain, D. T. Nair
Date :  05 Jun 10  (Deposition) - 08 Dec 10  (Release) - 08 Dec 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Endonuclease, Repair, Dimer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Namadurai, D. Jain, D. S. Kulkarni, C. R. Tabib, P. Friedhoff, D. N. Rao, D. T. Nair
The C-Terminal Domain Of The Mutl Homolog From Neisseria Gonorrhoeae Forms An Inverted Homodimer
Plos One V. 5 E1372 2010
PubMed-ID: 21060849  |  Reference-DOI: 10.1371/JOURNAL.PONE.0013726

(-) Compounds

Molecule 1 - DNA MISMATCH REPAIR PROTEIN MUTL
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES IN UNP 460-658
    Gene: MUTL, NGO0744, NGOL
    Organism Scientific: NEISSERIA GONORRHOEAE
    Organism Taxid: 242231
    Strain: FA1090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NCV)

(-) Sites  (0, 0)

(no "Site" information available for 3NCV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NCV)

(-) 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:187
 aligned with MUTL_NEIG1 | Q5F8M6 from UniProtKB/Swiss-Prot  Length:658

    Alignment length:192
                                   472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652  
           MUTL_NEIG1   463 ELPPLGFAIAQLLGIYILAQAEDSLLLIDMHAAAERVNYEKMKRQRQENGNLQSQHLLIPVTFAASHEECAALADHAETLAGFGLELSDMGGNTLAVRAAPVMLGKSDVVSLARDVLGELAQVGSSQTIASHENRILATMSCHGSIRAGRRLTLPEMNALLRDMENTPRSNQCNHGRPTWVKLTLKELDTLF 654
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeeeee...eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee.hhhhhhhhhhhhhhhhhh..eee.....eeeeeeee......hhhhhhhhhhhhhh...-----..hhhhhhhhhh...........hhhhhhhhhhhhhh.............eeeeehhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ncv A 463 ELPPLGFAIAQLLGIYILAQAEDSLLLIDMHAAAERVNYEKMKRQRQENGNLQSQHLLIPVTFAASHEECAALADHAETLAGFGLELSDMGGNTLAVRAAPVMLGKSDVVSLARDVLGELAQVG-----ASHENRILATMSCHGSIRAGRRLTLPEMNALLRDMENTPRSNQCNHGRPTWVKLTLKELDTLF 654
                                   472       482       492       502       512       522       532       542       552       562       572       582   |   592       602       612       622       632       642       652  
                                                                                                                                                     586   592                                                              


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with MUTL_NEIG1 | Q5F8M6 from UniProtKB/Swiss-Prot  Length:658

    Alignment length:193
                                   473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653   
           MUTL_NEIG1   464 LPPLGFAIAQLLGIYILAQAEDSLLLIDMHAAAERVNYEKMKRQRQENGNLQSQHLLIPVTFAASHEECAALADHAETLAGFGLELSDMGGNTLAVRAAPVMLGKSDVVSLARDVLGELAQVGSSQTIASHENRILATMSCHGSIRAGRRLTLPEMNALLRDMENTPRSNQCNHGRPTWVKLTLKELDTLFLR 656
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --MutL_C-3ncvB01 B:466-614                                                                                                                             ------------------------------------------ Pfam domains (1)
           Pfam domains (2) --MutL_C-3ncvB02 B:466-614                                                                                                                             ------------------------------------------ Pfam domains (2)
         Sec.struct. author .....eeeee....eeeeee..eeeeeehhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee.hhhhhhhhhhhhhhhhhh..eeee....eeeeeeee.hhh..hhhhhhhhhhhhhhh..-----..hhhhhhhhhhh..........hhhhhhhhhhhhhh.............eeeeehhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ncv B 464 LPPLGFAIAQLLGIYILAQAEDSLLLIDMHAAAERVNYEKMKRQRQENGNLQSQHLLIPVTFAASHEECAALADHAETLAGFGLELSDMGGNTLAVRAAPVMLGKSDVVSLARDVLGELAQVG-----ASHENRILATMSCHGSIRAGRRLTLPEMNALLRDMENTPRSNQCNHGRPTWVKLTLKELDTLFLR 656
                                   473       483       493       503       513       523       533       543       553       563       573       583  |    593       603       613       623       633       643       653   
                                                                                                                                                    586   592
   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 3NCV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MUTL_NEIG1 | Q5F8M6)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0030983    mismatched DNA binding    Interacting selectively and non-covalently with double-stranded DNA containing one or more mismatches.
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.

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 Related Entries

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