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(-) Description

Title :  LEXA G85D MUTANT
 
Authors :  Y. Luo, R. A. Pfuetzner, S. Mosimann, J. W. Little, N. C. J. Strynadka
Date :  27 Jun 01  (Deposition) - 19 Sep 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lexa Sos Repressor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Luo, R. A. Pfuetzner, S. Mosimann, M. Paetzel, E. A. Frey, M. Cherney, B. Kim, J. W. Little, N. C. Strynadka
Crystal Structure Of Lexa: A Conformational Switch For Regulation Of Self-Cleavage.
Cell(Cambridge, Mass. ) V. 106 585 2001
PubMed-ID: 11551506  |  Reference-DOI: 10.1016/S0092-8674(01)00479-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LEXA REPRESSOR
    Chains: A, B
    EC Number: 3.4.21.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LEXA
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:27 , ARG A:28 , SER A:63 , ARG A:64 , HOH A:420 , ARG B:140BINDING SITE FOR RESIDUE SO4 A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:106 -Pro A:107
2Lys B:106 -Pro B:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_LEXA_ECOLI_001 *G85DLEXA_ECOLI  ---  ---AD85D
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JHF)

(-) Exons   (0, 0)

(no "Exon" information available for 1JHF)

(-) 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:197
 aligned with LEXA_ECOLI | P0A7C2 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       
           LEXA_ECOLI     2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRVAAGEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRN 198
               SCOP domains d1jhfa1 A:2-72 LexA repressor, N-terminal DNA-binding domain           d1jhfa2 A:73-198 LexA C-terminal domain                                                                                        SCOP domains
               CATH domains 1jhfA02 A:2-70 'winged helix' repressor DNA binding domain           ---------1jhfA01 A:80-198 Umud Fragment, subunit A                                                                               CATH domains
               Pfam domains LexA_DNA_bind-1jhfA01 A:2-65                                    ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh...hhhhhhhhh...hhhhhhhhhhhhhhh..eee.......eee.......eeee..........hhh.eeeee..hhhhh.....eeee.....hhhhh.....eeeeee........eeeeee..eeeeeeeeee..eeeee........eeee.....eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------D----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jhf A   2 KALTARQQEVFDLIRDHISQTGMPPTRAEIAQRLGFRSPNAAEEHLKALARKGVIEIVSGASRGIRLLQEEEEGLPLVGRVAADEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRN 198
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       


Chain B from PDB  Type:PROTEIN  Length:111
 aligned with LEXA_ECOLI | P0A7C2 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:125
                                    84        94       104       114       124       134       144       154       164       174       184       194     
           LEXA_ECOLI    75 GLPLVGRVAAGEPLLAQQHIEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRNG 199
               SCOP domains d1jhf              b_ B: LexA C-terminal domain                                                                               SCOP domains
               CATH domains 1jhfB              00 B:75-199 Umud Fragment, subunit A                                                                       CATH domains
           Pfam domains (1) ---------------------------------------Peptidase_S24-1jhfB01 B:114-182                                      ----------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------Peptidase_S24-1jhfB02 B:114-182                                      ----------------- Pfam domains (2)
         Sec.struct. author .eee.--------------..eee..hhhhh.....eeee.....hhhhh.....eeeeee........eeeeee...eeeeeeeee..eeeee........eeee.....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jhf B  75 GLPLV--------------IEGHYQVDPSLFKPNADFLLRVSGMSMKDIGIMDGDLLAVHKTQDVRNGQVVVARIDDEVTVKRLKKQGNKVELLPENSEFKPIVVDLRQQSFTIEGLAVGVIRNG 199
                                |    -        94       104       114       124       134       144       154       164       174       184       194     
                               79             94
   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  (2, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: Peptidase_SF (8)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LEXA_ECOLI | P0A7C2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0009432    SOS response    An error-prone process for repairing damaged microbial DNA.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LEXA_ECOLI | P0A7C2: 1jhc 1jhe 1jhh 1lea 1leb 1mvd 1qaa 3jso 3jsp 3k3r

(-) Related Entries Specified in the PDB File

1jhc LEXA S119A C-TERMINAL TRYPTIC FRAGMENT
1jhe LEXA L89P Q92W E152A K156A MUTANT
1jhh LEXA S119A MUTANT