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(-) Description

Title :  CRYSTAL STRUCTURE OF THE LYSR-TYPE TRANSCRIPTIONAL REGULATOR TSAR
 
Authors :  D. Monferrer, T. Tralau, M. A. Kertesz, A. Kikhney, D. Svergun, I. Uson
Date :  21 Jan 09  (Deposition) - 26 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Lysr-Type, Transcriptional Regulator, Lttr, Tsar, Whth, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Monferrer, T. Tralau, M. A. Kertesz, I. Dix, M. Sola, I. Uson
Structural Studies On The Full-Length Lysr-Type Regulator Tsar From Comamonas Testosteroni T-2 Reveal A Novel Open Conformation Of The Tetrameric Lttr Fold
Mol. Microbiol. V. 75 1199 2010
PubMed-ID: 20059681  |  Reference-DOI: 10.1111/J.1365-2958.2010.07043.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSR TYPE REGULATOR OF TSAMBCD
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-70
    Expression System Strain: M10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TSAR
    Organism Common: PSEUDOMONAS TESTOSTERONI
    Organism Scientific: COMAMONAS TESTOSTERONI
    Organism Taxid: 285
    Strain: T-2
    Synonym: LYSR-TYPE TRANSCRIPTIONAL REGULATOR TSAR

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2CL2Ligand/IonCHLORIDE ION
3FMT2Ligand/IonFORMIC ACID
4GOL1Ligand/IonGLYCEROL
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
1BME8Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3FMT4Ligand/IonFORMIC ACID
4GOL2Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:256 , CYS A:257BINDING SITE FOR RESIDUE BME A 1002
2AC2SOFTWAREHIS A:176 , CYS A:190BINDING SITE FOR RESIDUE BME A 1003
3AC3SOFTWARECYS A:12 , LEU A:25 , HOH A:390BINDING SITE FOR RESIDUE BME A 1004
4AC4SOFTWARELEU A:227 , ASN A:250 , ALA A:251 , PHE A:252 , HOH A:334 , HOH A:403 , HOH A:465 , LEU B:104 , LEU B:246 , ARG B:249 , ASN B:250 , ALA B:251BINDING SITE FOR RESIDUE GOL A 2001
5AC5SOFTWARESER A:195 , SER A:196 , ILE A:204 , THR A:241 , MET A:242 , HOH A:311BINDING SITE FOR RESIDUE FMT A 3001
6AC6SOFTWAREGLN A:24 , VAL A:169 , ARG A:244 , SER A:258 , PRO A:260 , HOH A:349 , HOH A:437BINDING SITE FOR RESIDUE FMT A 3002
7AC7SOFTWAREHIS A:150 , PRO A:198 , ARG A:199BINDING SITE FOR RESIDUE CL A 4002
8AC8SOFTWARECYS B:190BINDING SITE FOR RESIDUE BME B 1001
9AC9SOFTWAREHIS B:150 , PRO B:198 , ARG B:199BINDING SITE FOR RESIDUE CL B 4001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:130 -Pro A:131
2Tyr B:130 -Pro B:131

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LYSRPS50931 LysR-type HTH domain profile.TSAR_COMTE1-58
 		  2A:3-59
B:3-59
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_LYSRPS50931 LysR-type HTH domain profile.TSAR_COMTE1-58
 		  4A:3-59
B:3-59

(-) Exons   (0, 0)

(no "Exon" information available for 3FXQ)

(-) 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:296
 aligned with TSAR_COMTE | P94678 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:296
                             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       259       269       279       289      
           TSAR_COMTE     - -MKLQTLQALICIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVSLTSFGQAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREFPDVTVNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHPMANATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLPEPKLGLVCESFLALPGVVAHSDLLTTMPRTLYERNAFKDQLCSIPLQDALPNPTIYVLRRHDLPVTPAAAGLIRWIQHHAL 295
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eee....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeehhhhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhh...eeeee.hhhhh...eeeeeeee..eeeeee.........hhhhhh..eeeee......hhhhhhhhhhh.....eeeeee....hhhhhhhh...eeeeehhhhhh..hhh.eee..........eeeeeee.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_LYSR  PDB: A:3-59 UniProt: 1-58                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fxq A   1 MLKLQTLQALICIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVSLTSFGQAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREFPDVTVNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHPMANATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLPEPKLGLVCESFLALPGVVAHSDLLTTMPRTLYERNAFKDQLCSIPLQDALPNPTIYVLRRHDLPVTPAAAGLIRWIQHHAL 296
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290      


Chain B from PDB  Type:PROTEIN  Length:296
 aligned with TSAR_COMTE | P94678 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:296
                             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       259       269       279       289      
           TSAR_COMTE     - -MKLQTLQALICIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVSLTSFGQAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREFPDVTVNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHPMANATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLPEPKLGLVCESFLALPGVVAHSDLLTTMPRTLYERNAFKDQLCSIPLQDALPNPTIYVLRRHDLPVTPAAAGLIRWIQHHAL 295
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...eeee..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhhhhhhhhhhhhhhhhhhh..eeeeeee.....hhhhhhh....eeeee.........eeeeeeee..eeeeee.........hhhhhh..eeee.......hhhhhhhhhhh.....eeeee.....hhhhhhhh....eeeehhhhhh..hhh.eee..........eeeeeee.....hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_LYSR  PDB: B:3-59 UniProt: 1-58                       --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3fxq B   1 MLKLQTLQALICIEEVGSLRAAAQLLHLSQPALSAAIQQLEDELKAPLLVRTKRGVSLTSFGQAFMKHARLIVTESRRAQEEIGQLRGRWEGHITFAASPAIALAALPLALASFAREFPDVTVNVRDGMYPAVSPQLRDGTLDFALTAAHKHDIDTDLEAQPLYVSDVVIVGQRQHPMANATRLAELQECRWAFSSAPRGPGAIIRNAFARYGLPEPKLGLVCESFLALPGVVAHSDLLTTMPRTLYERNAFKDQLCSIPLQDALPNPTIYVLRRHDLPVTPAAAGLIRWIQHHAL 296
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290
   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 3FXQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TSAR_COMTE | P94678)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        TSAR_COMTE | P94678: 3fxr 3fxu 3fzj 3n6t 3n6u

(-) Related Entries Specified in the PDB File

3fxr 3fxu 3fzj