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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MECI-MECA REPRESSOR-OPERATOR COMPLEX
 
Authors :  M. K. Safo, T. -P. Ko, F. N. Musayev, Q. Zhao, A. H. -J. Wang, G. L. Archer
Date :  09 Oct 05  (Deposition) - 25 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Methicillin, B-Lactam, Oligonucleotide Binding Domain, Dimerization Helical Domain, Repressor, Pseudo-Dyad Dna, Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. K. Safo, T. P. Ko, F. N. Musayev, Q. Zhao, A. H. Wang, G. L. Archer
Structure Of The Meci Repressor From Staphylococcus Aureus In Complex With The Cognate Dna Operator Of Mec.
Acta Crystallogr. , Sect. F V. 62 320 2006
PubMed-ID: 16582476  |  Reference-DOI: 10.1107/S1744309106009742
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'- D(P*TP*AP*CP*TP*AP*CP*AP*TP*AP*TP*GP*TP*AP*GP*TP*A)-3'
    ChainsE, F, G, H
    EngineeredYES
    SyntheticYES
 
Molecule 2 - METHICILLIN RESISTANCE REGULATORY PROTEIN MECI
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3
    Expression System StrainB834 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMECI
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid1280

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2D45)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D45)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D45)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D45)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D45)

(-) Exons   (0, 0)

(no "Exon" information available for 2D45)

(-) 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:117
 aligned with MECI_STAAN | P68261 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:117
                                    14        24        34        44        54        64        74        84        94       104       114       
           MECI_STAAN     5 TYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILN 121
               SCOP domains d2d45a1 A:5-121 Methicillin resistance regulatory protein MecI                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh..eehhhhhhhhhh.....hhhhhhhhhhhhhhh..ee.........eee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2d45 A   5 TYEISSAEWEVmNIIWmKKYASANNIIEEIQmQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILN 121
                                    14 |    | 24        34 |      44        54        64        74        84        94       104       114       
                                      16-MSE|             36-MSE                                                                                 
                                           21-MSE                                                                                                

Chain B from PDB  Type:PROTEIN  Length:119
 aligned with MECI_STAAN | P68261 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:119
                                    12        22        32        42        52        62        72        82        92       102       112         
           MECI_STAAN     3 NKTYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILN 121
               SCOP domains --d2d45b1 B:5-121 Methicillin resistance regulatory protein MecI                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhheeehhhhhhhhh.....hhhhhhhhhhhhhhhh.ee........eeee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2d45 B   3 NKTYEISSAEWEVmNIIWmKKYASANNIIEEIQmQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILN 121
                                    12   |    22        32   |    42        52        62        72        82        92       102       112         
                                        16-MSE|             36-MSE                                                                                 
                                             21-MSE                                                                                                

Chain C from PDB  Type:PROTEIN  Length:117
 aligned with MECI_STAAN | P68261 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:117
                                    14        24        34        44        54        64        74        84        94       104       114       
           MECI_STAAN     5 TYEISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILN 121
               SCOP domains d2d45c1 C:5-121 Methicillin resistance regulatory protein MecI                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhheeehhhhhhhhh.....hhhhhhhhhhhhhhhh.ee........eeee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 2d45 C   5 TYEISSAEWEVmNIIWmKKYASANNIIEEIQmQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILN 121
                                    14 |    | 24        34 |      44        54        64        74        84        94       104       114       
                                      16-MSE|             36-MSE                                                                                 
                                           21-MSE                                                                                                

Chain D from PDB  Type:PROTEIN  Length:115
 aligned with MECI_STAAN | P68261 from UniProtKB/Swiss-Prot  Length:123

    Alignment length:115
                                    16        26        36        46        56        66        76        86        96       106       116     
           MECI_STAAN     7 EISSAEWEVMNIIWMKKYASANNIIEEIQMQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILN 121
               SCOP domains d2d45d1 D:7-121 Methicillin resistance regulatory protein MecI                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhheeehhhhhhhhh.....hhhhhhhhhhhhhhhh.ee........eeee..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2d45 D   7 EISSAEWEVmNIIWmKKYASANNIIEEIQmQKDWSPKTIRTLITRLYKKGFIDRKKDNKIFQYYSLVEESDIKYKTSKNFINKVYKGGFNSLVLNFVEKEDLSQDEIEELRNILN 121
                                    16    |   26        36        46        56        66        76        86        96       106       116     
                                    16-MSE|             36-MSE                                                                                 
                                         21-MSE                                                                                                

Chain E from PDB  Type:DNA  Length:16
                                                
                 2d45 E 201 TACTACATATGTAGTA 216
                                   210      

Chain F from PDB  Type:DNA  Length:16
                                                
                 2d45 F 201 TACTACATATGTAGTA 216
                                   210      

Chain G from PDB  Type:DNA  Length:13
                                             
                 2d45 G 201 TACTACATATGTA 213
                                   210   

Chain H from PDB  Type:DNA  Length:12
                                            
                 2d45 H 205 ACATATGTAGTA 216
                                   214  

   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  (1, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D45)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D45)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MECI_STAAN | P68261)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MECI_STAAN | P682611okr 1sax 1sd6 1sd7

(-) Related Entries Specified in the PDB File

1sd6 DNA-FREE REPRESSOR (NATIVE)
1sd7 DNA-FREE REPRESSOR (SEMET DERIVATIVE)
1xsd SAME DNA OPERATOR OF MECA BUT COMPLEXED WITH BLAI REPRESSOR