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(-) Description

Title :  CRYSTAL STRUCTURE OF A LEXA PROTEIN FROM THERMOTOGA MARITIMA
 
Authors :  A. P. P. Zhang, P. A. Rice
Date :  30 Sep 09  (Deposition) - 06 Oct 10  (Release) - 06 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.37
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Winged Helix-Turn-Helix, Repressor, Lexa, Sos System, Autocatalytic Cleavage, Dna Damage, Dna Repair, Dna Replication, Dna-Binding, Hydrolase, Sos Response, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. P. Zhang, P. A. Rice
Crystal Structure Of A Lexa Protein From Thermotoga Maritim
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LEXA REPRESSOR
    Chains: A, B
    EC Number: 3.4.21.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: LEXA, TM_1082
    Mutation: YES
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 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
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:29 , ARG B:87 , GLU B:88 , ALA B:89 , LYS B:185 , HOH B:218BINDING SITE FOR RESIDUE GOL B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K2Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K2Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K2Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3K2Z)

(-) 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:192
 aligned with LEXA_THEMA | O33927 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     
           LEXA_THEMA     3 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKKGYIERKNGKPRALRISKSIRNKIPLIGEIRAGEKREAIEYLEDYIEIPESFLSSGYDHFLLKVKGESMIEEHICDGDLVLVRRQDWAQNGDIVAAMVDGEVTLKKFYQRGDTVELRPANREMSSMFFRAEKVKILGKVVGVFRKL 197
               SCOP domains d3k2za1 A:3-71 automated matches                                     d3k2za2 A:72-197 automated matches                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..ee.---.....ee......eeeeeeeeee.hhh.eeeeeeeeee.hhhhh.....eeeee.....hhhhh.....eeeeee........eeeeee..eeeeeeeeee..eeeee........eeee.hhheeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2z A   3 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKKGYIER---KPRALRISKSIRNKIPLIGEIRAGEKREAIEYLEDYIEIPESFLSSGYDHFLLKVKGESMIEEHICDGDLVLVRRQDWAQNGDIVAAMVDGEVTLAKFYQRGDTVELRPANREMSSMFFRAEKVKILGKVVGVFRKL 197
                                    12        22        32        42        52    |   62        72        82        92       102       112       122       132       142       152       162       172       182       192     
                                                                                 57  61                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with LEXA_THEMA | O33927 from UniProtKB/Swiss-Prot  Length:197

    Alignment length:195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     
           LEXA_THEMA     3 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKKGYIERKNGKPRALRISKSIRNKIPLIGEIRAGEKREAIEYLEDYIEIPESFLSSGYDHFLLKVKGESMIEEHICDGDLVLVRRQDWAQNGDIVAAMVDGEVTLKKFYQRGDTVELRPANREMSSMFFRAEKVKILGKVVGVFRKL 197
               SCOP domains d3k2zb1 B:3-71 automated matches                                     d3k2zb2 B:72-197 automated matches                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) LexA_DNA_bind-3k2zB01 B:3-64                                  -------------------------------------------------Peptidase_S24-3k2zB03 B:114-182                                      --------------- Pfam domains (1)
           Pfam domains (2) LexA_DNA_bind-3k2zB02 B:3-64                                  -------------------------------------------------Peptidase_S24-3k2zB04 B:114-182                                      --------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eehhhhhhhhhee......eeeeeeeeee.....eeeeeeeeee.hhhhh.....eeeee.....hhhhh.....eeeeee........eeeeee..eeeeeeeeee..eeeee........eeee.hhheeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k2z B   3 DLTERQRKVLLFIEEFIEKNGYPPSVREIARRFRITPRGALLHLIALEKKGYIERKNGKPRALRISKSIRNKIPLIGEIRAGEKREAIEYLEDYIEIPESFLSSGYDHFLLKVKGESMIEEHICDGDLVLVRRQDWAQNGDIVAAMVDGEVTLAKFYQRGDTVELRPANREMSSMFFRAEKVKILGKVVGVFRKL 197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
   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, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K2Z)

(-) Pfam Domains  (2, 4)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LEXA_THEMA | O33927)
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.

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