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(-) Description

Title :  STRUCTURE OF THE N-TERMINAL DOMAIN OF THE E. COLI ANTITOXIN MQSA (YGIT/B3021) IN COMPLEX WITH THE E. COLI TOXIN MQSR (YGIU/B3022)
 
Authors :  S. Grigoriu, B. L. Brown, J. M. Arruda, W. Peti, R. Page
Date :  18 May 09  (Deposition) - 12 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Toxin-Antitoxin System, Zn-Binding Protein, Mqsr, Mqsa, Ygiu, Ygit, B3022, B3021, Stress Response, Quorum Sensing, Dna Binding Protein- Toxin Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Brown, S. Grigoriu, Y. Kim, J. M. Arruda, A. Davenport, T. K. Wood, W. Peti, R. Page
Three Dimensional Structure Of The Mqsr:Mqsa Complex: A Novel Ta Pair Comprised Of A Toxin Homologous To Rele And A Antitoxin With Unique Properties.
Plos Pathog. V. 5 E1000 2009
PubMed-ID: 20041169  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1000706

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR MQSA(YGIT)
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCA21A
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: MQSA N-TERMINAL DOMAIN
    Gene: B3021, JW2989, YGIT
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: ESCHERICHIA COLI STR. K12
 
Molecule 2 - MOTILITY QUORUM-SENSING REGULATOR MQSR
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A(+)
    Expression System Strain: BL21 DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B3022, JW2990, MQSR, YGIU
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: ESCHERICHIA COLI STR. K12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:3 , CYS A:6 , CYS A:37 , CYS A:40BINDING SITE FOR RESIDUE ZN A 121
2AC2SOFTWAREPHE A:22 , ARG A:23 , ASN A:65 , GLU B:34 , LEU B:35 , GLY B:36 , HOH B:124BINDING SITE FOR RESIDUE GOL A 3968
3AC3SOFTWAREASN A:46 , ARG B:23 , VAL B:90 , HOH B:102 , HOH B:218 , GLY D:36BINDING SITE FOR RESIDUE GOL B 3968
4AC4SOFTWARECYS C:3 , CYS C:6 , CYS C:37 , CYS C:40BINDING SITE FOR RESIDUE ZN C 121

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HI2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HI2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HI2)

(-) Exons   (0, 0)

(no "Exon" information available for 3HI2)

(-) Sequences/Alignments

Asymmetric 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:70
 aligned with MQSA_ECOLI | Q46864 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:70
                                    10        20        30        40        50        60        70
            MQSA_ECOLI    1 MKCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVNAETVA 70
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeeeee..eeeeeeeeeeeee.....ee.hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                  3hi2 A  1 MKCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVNAETVA 70
                                    10        20        30        40        50        60        70


Chain B from PDB  Type:PROTEIN  Length:97
 aligned with MQSR_ECOLI | Q46865 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:97
                                    10        20        30        40        50        60        70        80        90       
            MQSR_ECOLI    1 MEKRTPHTRLSQVKKLVNAGQVRTTRSALLNADELGLDFDGMCNVIIGLSESDFYKSMTTYSDHTIWQDVYRPRLVTGQVYLKITVIHDVLIVSFKE 97
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....hhhhhhhhhhh..eeeehhhhhhhhhh..hhhhhhhhhhh.hhh.eeeee.........eeee..ee..ee..eeeeee..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                  3hi2 B  1 MEKRTPHTRLSQVKKLVNAGQVRTTRSALLNADELGLDFDGMCNVIIGLSESDFYKSMTTYSDHTIWQDVYRPRLVTGQVYLKITVIHDVLIVSFKE 97
                                    10        20        30        40        50        60        70        80        90       


Chain C from PDB  Type:PROTEIN  Length:59
 aligned with MQSA_ECOLI | Q46864 from UniProtKB/Swiss-Prot  Length:131

    Alignment length:65
                                    10        20        30        40        50        60     
            MQSA_ECOLI    1 MKCPVCHQGEMVSGIKDIPYTFRGRKTVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVN 65
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee------eeeeeeeeeee.....ee.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                  3hi2 C  1 MKCPVCHQGEMVSGIKDIPY------TVLKGIHGLYCVHCEESIMNKEESDAFMAQVKAFRASVN 65
                                    10        20      | 30        40        50        60     
                                              20     27                                      


Chain D from PDB  Type:PROTEIN  Length:91
 aligned with MQSR_ECOLI | Q46865 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:94
                                    11        21        31        41        51        61        71        81        91    
            MQSR_ECOLI    2 EKRTPHTRLSQVKKLVNAGQVRTTRSALLNADELGLDFDGMCNVIIGLSESDFYKSMTTYSDHTIWQDVYRPRLVTGQVYLKITVIHDVLIVSF 95
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhh..eeeehhhhhhhhhh..hhhhhhhhhhh.hhh.eeeee..---....eeee..ee..ee..eeeeee..eeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3hi2 D  2 EKRTPHTRLSQVKKLVNAGQVRTTRSALLNADELGLDFDGMCNVIIGLSESDFYKSMTT---HTIWQDVYRPRLVTGQVYLKITVIHDVLIVSF 95
                                    11        21        31        41        51        |-  |     71        81        91    
                                                                                     60  64
   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 3HI2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HI2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HI2)

(-) Gene Ontology  (18, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (MQSA_ECOLI | Q46864)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    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.

Chain B,D   (MQSR_ECOLI | Q46865)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0004521    endoribonuclease activity    Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    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:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0009372    quorum sensing    The process in which single-celled organisms monitor their population density by detecting the concentration of small, diffusible signal molecules produced by the cells themselves.
    GO:2000145    regulation of cell motility    Any process that modulates the frequency, rate or extent of cell motility.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0044010    single-species biofilm formation    A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MQSA_ECOLI | Q46864: 2kz8 3fmy 3ga8 3gn5 3o9x

(-) Related Entries Specified in the PDB File

3fmy STRUCTURE OF THE C-TERMINAL DOMAIN OF THE E. COLI PROTEIN MQSA (YGIT/B3021)
3ga8 STRUCTURE OF THE N-TERMINAL DOMAIN OF THE E. COLI PROTEIN MQSA (YGIT/B3021)
3gn5 STRUCTURE OF THE E. COLI PROTEIN MQSA (YGIT/B3021)