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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE TRANSCRIPTIONAL REGULATOR CONTAINING A LUXR DNA BINDING DOMAIN (NP_811094.1) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.04 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  19 Mar 08  (Deposition) - 01 Apr 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Np_811094. 1, Putative Transcriptional Regulator Containing A Luxr Dna Binding Domain, Bacterial Regulatory Proteins, Luxr Family, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Dna-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Putative Transcriptional Regulator Containing A Luxr Dna Binding Domain (Np_811094. 1) From Bacteroides Thetaiotaomicron Vpi-5482 At 2. 04 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Atcc: 29148
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NP_811094.1, BT_2181
    Organism Scientific: BACTEROIDES THETAIOTAOMICRON VPI-5482
    Organism Taxid: 226186
    Strain: VPI-5482 / DSM 2079 / NCTC 10582 / E50

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 37)

Asymmetric Unit (4, 37)
No.NameCountTypeFull Name
1CL7Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE27Mod. Amino AcidSELENOMETHIONINE
4NA2Ligand/IonSODIUM ION
Biological Unit 1 (1, 18)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3MSE18Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MSE18Mod. Amino AcidSELENOMETHIONINE
4NA-1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU C:169 , GLY C:171BINDING SITE FOR RESIDUE NA C 258
02AC2SOFTWAREARG C:181BINDING SITE FOR RESIDUE NA C 259
03AC3SOFTWAREPHE C:65 , GLN C:136BINDING SITE FOR RESIDUE CL C 260
04AC4SOFTWAREPHE B:65 , GLN B:136BINDING SITE FOR RESIDUE CL B 258
05AC5SOFTWARELYS A:215 , LYS B:210 , TYR C:135BINDING SITE FOR RESIDUE CL A 258
06AC6SOFTWAREILE A:223 , SER A:224 , THR A:227 , TYR C:173 , THR C:186BINDING SITE FOR RESIDUE CL A 259
07AC7SOFTWAREASN A:64 , PHE A:65 , GLN A:136BINDING SITE FOR RESIDUE CL A 260
08AC8SOFTWARESER C:76 , ASP C:79BINDING SITE FOR RESIDUE CL C 261
09AC9SOFTWAREARG B:125 , GLU B:169BINDING SITE FOR RESIDUE CL B 259
10BC1SOFTWAREGLN C:29 , HIS C:30 , PHE C:33 , SER C:36 , GLU C:39BINDING SITE FOR RESIDUE GOL C 262

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3CLO)

(-) 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:258
 aligned with Q8A5Q7_BACTN | Q8A5Q7 from UniProtKB/TrEMBL  Length:257

    Alignment length:258
                             1                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249        
         Q8A5Q7_BACTN     - -MDVLQKEIDEVYATHPTAHEALDNGIVEQHQQFVRSLTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSMDEDCIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTPAGNVWLIFCLYSLSADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELMKLL 257
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3cloA01 A:0-193  [code=3.30.450.20, no name defined]                                                                                                                                              3cloA02 A:194-257 'winged helix' repressor DNA binding domain    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.eeeeee....eeeeee...hhhhh.hhhhhhh.ee....hhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeee.....eeeeeeeeeeeee.....eeeeeeeeee............eeee....eeee..hhhhhh...hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3clo A   0 GmDVLQKEIDEVYATHPTAHEALDNGIVEQHQQFVRSLTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSmDEDCIYRRIHPEDLVEKRLmEYKFFQKTFSmSPGERLKYRGRCRLRmmNEKGVYQYIDNLVQImQNTPAGNVWLIFCLYSLSADQRPEQGIYATITQmERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELmKLL 257
                             |       9        19        29        39        49        59        69        79 |      89        99 |     109  |    119       129       139     | 149       159       169       179       189       199       209       219       229       239       249    |   
                             |                                                                              81-MSE             101-MSE    112-MSE         128-MSE          145-MSE                           179-MSE                                                                    254-MSE
                             1-MSE                                                                                                                         129-MSE                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:258
 aligned with Q8A5Q7_BACTN | Q8A5Q7 from UniProtKB/TrEMBL  Length:257

    Alignment length:258
                             1                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249        
         Q8A5Q7_BACTN     - -MDVLQKEIDEVYATHPTAHEALDNGIVEQHQQFVRSLTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSMDEDCIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTPAGNVWLIFCLYSLSADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELMKLL 257
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3cloB01 B:0-193  [code=3.30.450.20, no name defined]                                                                                                                                              3cloB02 B:194-257 'winged helix' repressor DNA binding domain    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.eeeeee....eeeeee...hhhhh.hhhhhh..ee....hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeee.....eeeeeeeeeeeee.....eeeeeeeeee............eeee....eeee..hhhhhh...hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3clo B   0 GmDVLQKEIDEVYATHPTAHEALDNGIVEQHQQFVRSLTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSmDEDCIYRRIHPEDLVEKRLmEYKFFQKTFSmSPGERLKYRGRCRLRmmNEKGVYQYIDNLVQImQNTPAGNVWLIFCLYSLSADQRPEQGIYATITQmERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELmKLL 257
                             |       9        19        29        39        49        59        69        79 |      89        99 |     109  |    119       129       139     | 149       159       169       179       189       199       209       219       229       239       249    |   
                             |                                                                              81-MSE             101-MSE    112-MSE         128-MSE          145-MSE                           179-MSE                                                                    254-MSE
                             1-MSE                                                                                                                         129-MSE                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:257
 aligned with Q8A5Q7_BACTN | Q8A5Q7 from UniProtKB/TrEMBL  Length:257

    Alignment length:258
                             1                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249        
         Q8A5Q7_BACTN     - -MDVLQKEIDEVYATHPTAHEALDNGIVEQHQQFVRSLTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSMDEDCIYRRIHPEDLVEKRLMEYKFFQKTFSMSPGERLKYRGRCRLRMMNEKGVYQYIDNLVQIMQNTPAGNVWLIFCLYSLSADQRPEQGIYATITQMERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELMKLL 257
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3cloC01 C:0-193  [code=3 .30.450.20, no name defined]                                                                                                                                             3cloC02 C:194-257 'winged helix' repressor DNA binding domain    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh...-hhhhhhhhhhhhhhhhhh.eeeeee....eeeeee...hhhhh.hhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeee.....eeeeeeeeeeeee.....eeeeeeeeee............eeee....eeee..hhhhhh...hhhhhhhhhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3clo C   0 GmDVLQKEIDEVYATHPTAHEALD-GIVEQHQQFVRSLTEVNGGCAVISDLSNRKSYVTVHPWANFLGLTPEEAALSVIDSmDEDCIYRRIHPEDLVEKRLmEYKFFQKTFSmSPGERLKYRGRCRLRmmNEKGVYQYIDNLVQImQNTPAGNVWLIFCLYSLSADQRPEQGIYATITQmERGEVETLSLSEEHRNILSEREKEILRCIRKGLSSKEIAATLYISVNTVNRHRQNILEKLSVGNSIEACRAAELmKLL 257
                             |       9        19   | |  29        39        49        59        69        79 |      89        99 |     109  |    119       129       139     | 149       159       169       179       189       199       209       219       229       239       249    |   
                             |                    23 |                                                      81-MSE             101-MSE    112-MSE         128-MSE          145-MSE                           179-MSE                                                                    254-MSE
                             1-MSE                  25                                                                                                     129-MSE
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  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 3CLO)

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8A5Q7_BACTN | Q8A5Q7)
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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