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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE TETR/ACRR FAMILY TRANSCRIPTIONAL REGULATOR (SARO_0558) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM AT 1.80 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  17 Sep 07  (Deposition) - 16 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Bacterial Regulatory Proteins, Tetr Family, Dna-Binding, Dna/Rna- Binding 3-Helical Bundle Fold, Helix Turn Helix Motif, Hth Motif, Transcription Regulator, Transcription Regulation, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Predicted Transcriptional Regulator Of Tetr/Acrr Family (Yp_495839. 1) From Novosphingobium Aromaticivorans Dsm 12444 At 1. 80 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR, TETR FAMILY
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YP_495839.1, SARO_0558
    Organism Scientific: NOVOSPHINGOBIUM AROMATICIVORANS
    Organism Taxid: 279238
    Strain: DSM 12444

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 36)

Asymmetric/Biological Unit (3, 36)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO14Ligand/Ion1,2-ETHANEDIOL
3MSE20Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:178 , SER B:157 , GLN B:161 , HOH B:348BINDING SITE FOR RESIDUE CL A 212
02AC2SOFTWARESER A:157 , GLN A:161 , HOH A:376 , ARG B:178BINDING SITE FOR RESIDUE CL A 213
03AC3SOFTWAREASP A:153 , GLU A:154 , SER A:157 , LYS B:183 , HOH B:225 , HOH B:241BINDING SITE FOR RESIDUE EDO B 212
04AC4SOFTWAREGLU A:154 , LYS B:183 , ARG B:186 , HOH B:237 , HOH B:243BINDING SITE FOR RESIDUE EDO B 213
05AC5SOFTWARELYS A:183 , ARG A:186 , LEU B:150 , GLU B:154BINDING SITE FOR RESIDUE EDO B 214
06AC6SOFTWARELEU A:77 , LYS A:86 , GLU A:136 , GLU A:140 , HOH A:231BINDING SITE FOR RESIDUE EDO A 214
07AC7SOFTWAREHOH A:267 , HOH A:350 , VAL B:70 , SER B:125 , LEU B:129 , HOH B:319BINDING SITE FOR RESIDUE EDO A 215
08AC8SOFTWAREARG A:124 , HOH A:240 , GLY B:135 , GLU B:136 , VAL B:152 , HOH B:258 , HOH B:286BINDING SITE FOR RESIDUE EDO B 215
09AC9SOFTWAREVAL A:152 , HOH A:333 , GLU B:121 , EDO B:218 , HOH B:240 , HOH B:294BINDING SITE FOR RESIDUE EDO B 216
10BC1SOFTWAREARG A:94 , ALA A:130 , CYS A:167 , HOH A:358 , HOH A:394 , HOH A:404BINDING SITE FOR RESIDUE EDO A 216
11BC2SOFTWARELYS A:183 , HOH A:406 , ASP B:153 , GLU B:154 , SER B:157BINDING SITE FOR RESIDUE EDO A 217
12BC3SOFTWAREASP A:193 , SER A:196 , ARG A:200 , HOH A:304BINDING SITE FOR RESIDUE EDO A 218
13BC4SOFTWAREASP B:193 , ARG B:200 , HOH B:298BINDING SITE FOR RESIDUE EDO B 217
14BC5SOFTWAREGLY A:201 , SER A:204BINDING SITE FOR RESIDUE EDO A 219
15BC6SOFTWAREMSE A:142 , SER A:143 , HOH A:222 , PHE B:120 , EDO B:216 , HOH B:294BINDING SITE FOR RESIDUE EDO B 218
16BC7SOFTWARESER A:125 , LEU A:129 , HOH A:301 , HIS B:132 , GLU B:136 , HOH B:381BINDING SITE FOR RESIDUE EDO B 219

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RAS)

(-) 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:200
 aligned with Q2GAW8_NOVAD | Q2GAW8 from UniProtKB/TrEMBL  Length:211

    Alignment length:200
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204
         Q2GAW8_NOVAD     5 GTEHDAMRARLVDVAQAIVEERGGAGLTLSELAARAGISQANLSRYFETREDLMEAIADYWFHPMVEIMEDVLASDLPPRRKMYEFFARRFVVMRRKWEADPVKLQTYIEVGNDYFEQVRSYIDLADHYLGEIIGEAMSDGAFSGLEVDETISLVNQMCAPYCALNTMTTFMERLSEDKLARIVDAVFDGLSAQDRGARS 204
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rasA01 A:5-195 Tetracycline Repressor, domain 2                                                                                                                                               --------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ras A   5 GTEHDAmRARLVDVAQAIVEERGGAGLTLSELAARAGISQANLSRYFETREDLmEAIADYWFHPmVEImEDVLASDLPPRRKmYEFFARRFVVmRRKWEADPVKLQTYIEVGNDYFEQVRSYIDLADHYLGEIIGEAmSDGAFSGLEVDETISLVNQmCAPYCALNTmTTFmERLSEDKLARIVDAVFDGLSAQDRGARS 204
                                  | 14        24        34        44        54   |    64    |   74        84  |     94   |   104       114       124       134       144       154       164       174 |     184       194       204
                                 11-MSE                                         58-MSE     69-MSE            87-MSE     98-MSE                                     142-MSE             162-MSE   172-MSE                            
                                                                                               73-MSE                                                                                                176-MSE                        


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with Q2GAW8_NOVAD | Q2GAW8 from UniProtKB/TrEMBL  Length:211

    Alignment length:204
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204    
         Q2GAW8_NOVAD     5 GTEHDAMRARLVDVAQAIVEERGGAGLTLSELAARAGISQANLSRYFETREDLMEAIADYWFHPMVEIMEDVLASDLPPRRKMYEFFARRFVVMRRKWEADPVKLQTYIEVGNDYFEQVRSYIDLADHYLGEIIGEAMSDGAFSGLEVDETISLVNQMCAPYCALNTMTTFMERLSEDKLARIVDAVFDGLSAQDRGARSLTGL 208
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2rasB01 B:5-195 Tetracycline Repressor, domain 2                                                                                                                                               ------------- CATH domains
           Pfam domains (1) ----------TetR_N-2rasB01 B:15-61                         --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------TetR_N-2rasB02 B:15-61                         --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ras B   5 GTEHDAmRARLVDVAQAIVEERGGAGLTLSELAARAGISQANLSRYFETREDLmEAIADYWFHPmVEImEDVLASDLPPRRKmYEFFARRFVVmRRKWEADPVKLQTYIEVGNDYFEQVRSYIDLADHYLGEIIGEAmSDGAFSGLEVDETISLVNQmCAPYCALNTmTTFmERLSEDKLARIVDAVFDGLSAQDRGARSLTGL 208
                                  | 14        24        34        44        54   |    64    |   74        84  |     94   |   104       114       124       134       144       154       164       174 |     184       194       204    
                                 11-MSE                                         58-MSE     69-MSE            87-MSE     98-MSE                                     142-MSE             162-MSE   172-MSE                                
                                                                                               73-MSE                                                                                                176-MSE
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  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 2RAS)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q2GAW8_NOVAD | Q2GAW8)
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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