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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MASTER TRANSCRIPTIONAL REGULATOR, SMCR, IN VIBRIO VULNIFICUS PROVIDES INSIGHT INTO ITS DNA RECOGNITION MECHANISM
 
Authors :  M. H. Kim, Y. Kim, W. -C. Choi, J. Hwang
Date :  08 Dec 09  (Deposition) - 16 Mar 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Vibrio Vulnificus, Smcr, Transcriptional Regulator, Quorum Sensing, Dna-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, B. S. Kim, Y. J. Park, W. -C. Choi, J. Hwang, B. S. Kang, T. -K. Oh, S. H. Choi, M. H. Kim
The Crystal Structure Of Smcr, A Quorum-Sensing Master Regulator Of Vibrio Vulnificus, Provides Insight Into Its Regulation Of Transcription
J. Biol. Chem. V. 285 14020 2010
PubMed-ID: 20178981  |  Reference-DOI: 10.1074/JBC.M109.100248

(-) Compounds

Molecule 1 - SMCR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHIS-PARALLEL1
    Expression System Strain: B834 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: VIBRIO VULNIFICUS
    Organism Taxid: 672
    Synonym: SMCR-LIKE PROTEIN, VVPR

 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, 23)

Asymmetric Unit (2, 23)
No.NameCountTypeFull Name
1MSE17Mod. Amino AcidSELENOMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR C:10 , ARG C:11 , LYS C:146 , ARG C:150 , HOH C:297BINDING SITE FOR RESIDUE SO4 C 206
2AC2SOFTWAREARG A:11 , ARG A:150 , HOH A:350BINDING SITE FOR RESIDUE SO4 A 206
3AC3SOFTWAREARG B:73 , HIS D:70 , ARG D:73 , GLN D:74 , HOH D:254BINDING SITE FOR RESIDUE SO4 D 206
4AC4SOFTWAREARG C:11 , LEU C:85 , ALA C:89 , ASN C:92 , MSE C:143 , ALA C:147 , ARG C:150 , GLU C:152BINDING SITE FOR RESIDUE SO4 C 207
5AC5SOFTWARETHR B:180 , ASN B:181 , ARG C:9 , LEU C:139 , ASN C:142 , HOH C:279BINDING SITE FOR RESIDUE SO4 B 206
6AC6SOFTWAREARG C:36 , ARG D:32 , ARG D:36BINDING SITE FOR RESIDUE SO4 D 207

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:198 -B:198
2B:154 -D:154
3C:198 -D:198

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KZ9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KZ9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KZ9)

(-) Exons   (0, 0)

(no "Exon" information available for 3KZ9)

(-) 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:201
 aligned with Q9L8G8_VIBVL | Q9L8G8 from UniProtKB/TrEMBL  Length:205

    Alignment length:201
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204 
         Q9L8G8_VIBVL     5 AKRPRTRLSPLKRKQQLMEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDLHAKENIANITNAMIELVVQDNHWLKVWFEWSASTRDEVWPLFVTTNRTNQLLVQNMFIKAIERGEVCDQHNPEDLANLFHGICYSLFVQANRTNNTAELSKLVSSYLDMLCIYKREHE 205
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kz9 A   5 AKRPRTRLSPLKRKQQLmEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDLHAKENIANITNAmIELVVQDNHWLKVWFEWSASTRDEVWPLFVTTNRTNQLLVQNmFIKAIERGEVCDQHNPEDLANLFHGICYSLFVQANRTNNTAELSKLVSSYLDmLCIYKREHE 205
                                    14       |24        34        44        54        64        74        84        94     | 104       114       124       134       144       154       164       174       184       194 |     204 
                                            22-MSE                                                                       100-MSE                                    143-MSE                                              196-MSE     


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with Q9L8G8_VIBVL | Q9L8G8 from UniProtKB/TrEMBL  Length:205

    Alignment length:203
                             1                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   
         Q9L8G8_VIBVL     - -MDSIAKRPRTRLSPLKRKQQLMEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDLHAKENIANITNAMIELVVQDNHWLKVWFEWSASTRDEVWPLFVTTNRTNQLLVQNMFIKAIERGEVCDQHNPEDLANLFHGICYSLFVQANRTNNTAELSKLVSSYLDMLCIYKR 202
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kz9 B   0 AmDSIAKRPRTRLSPLKRKQQLmEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDLHAKENIANITNAmIELVVQDNHWLKVWFEWSASTRDEVWPLFVTTNRTNQLLVQNmFIKAIERGEVCDQHNPEDLANLFHGICYSLFVQANRTNNTAELSKLVSSYLDmLCIYKR 202
                             |       9        19  |     29        39        49        59        69        79        89        99|      109       119       129       139   |   149       159       169       179       189      |199   
                             1-MSE               22-MSE                                                                       100-MSE                                    143-MSE                                              196-MSE  


Chain C from PDB  Type:PROTEIN  Length:203
 aligned with Q9L8G8_VIBVL | Q9L8G8 from UniProtKB/TrEMBL  Length:205

    Alignment length:203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   
         Q9L8G8_VIBVL     3 SIAKRPRTRLSPLKRKQQLMEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDLHAKENIANITNAMIELVVQDNHWLKVWFEWSASTRDEVWPLFVTTNRTNQLLVQNMFIKAIERGEVCDQHNPEDLANLFHGICYSLFVQANRTNNTAELSKLVSSYLDMLCIYKREHE 205
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kz9 C   3 SIAKRPRTRLSPLKRKQQLmEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDLHAKENIANITNAmIELVVQDNHWLKVWFEWSASTRDEVWPLFVTTNRTNQLLVQNmFIKAIERGEVCDQHNPEDLANLFHGICYSLFVQANRTNNTAELSKLVSSYLDmLCIYKREHE 205
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142|      152       162       172       182       192   |   202   
                                              22-MSE                                                                       100-MSE                                    143-MSE                                              196-MSE     


Chain D from PDB  Type:PROTEIN  Length:199
 aligned with Q9L8G8_VIBVL | Q9L8G8 from UniProtKB/TrEMBL  Length:205

    Alignment length:199
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194         
         Q9L8G8_VIBVL     5 AKRPRTRLSPLKRKQQLMEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDLHAKENIANITNAMIELVVQDNHWLKVWFEWSASTRDEVWPLFVTTNRTNQLLVQNMFIKAIERGEVCDQHNPEDLANLFHGICYSLFVQANRTNNTAELSKLVSSYLDMLCIYKRE 203
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kz9 D   5 AKRPRTRLSPLKRKQQLmEIALEVFARRGIGRGGHADIAEIAQVSVATVFNYFPTREDLVDEVLNHVVRQFSNFLSDNIDLDLHAKENIANITNAmIELVVQDNHWLKVWFEWSASTRDEVWPLFVTTNRTNQLLVQNmFIKAIERGEVCDQHNPEDLANLFHGICYSLFVQANRTNNTAELSKLVSSYLDmLCIYKRE 203
                                    14       |24        34        44        54        64        74        84        94     | 104       114       124       134       144       154       164       174       184       194 |       
                                            22-MSE                                                                       100-MSE                                    143-MSE                                              196-MSE
   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 3KZ9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KZ9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KZ9)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q9L8G8_VIBVL | Q9L8G8)
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: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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