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(-) Description

Title :  CRYSTAL STRUCTURE OF A TETR FAMILY TRANSCRIPTION REGULATOR (MAQU_1417) FROM MARINOBACTER AQUAEOLEI VT8 AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  19 Oct 10  (Deposition) - 17 Nov 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Tetr Family Transcription Regulator (Maqu_1417) From Marinobacter Aquaeolei Vt8 At 1. 90 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TETR FAMILY TRANSCRIPTION REGULATOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MAQU_1417
    Organism Common: MARINOBACTER HYDROCARBONOCLASTICUS (STRAIN DSM 11845)
    Organism Scientific: MARINOBACTER AQUAEOLEI
    Organism Taxid: 351348
    Strain: VT8

 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  (3, 32)

Asymmetric Unit (3, 32)
No.NameCountTypeFull Name
1ACT12Ligand/IonACETATE ION
2MSE15Mod. Amino AcidSELENOMETHIONINE
3PGO5Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1ACT7Ligand/IonACETATE ION
2MSE7Mod. Amino AcidSELENOMETHIONINE
3PGO4Ligand/IonS-1,2-PROPANEDIOL
Biological Unit 2 (3, 14)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2MSE8Mod. Amino AcidSELENOMETHIONINE
3PGO1Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:4 , SER A:7BINDING SITE FOR RESIDUE ACT A 201
02AC2SOFTWAREPRO A:99 , ARG A:103 , GLN A:163BINDING SITE FOR RESIDUE ACT A 205
03AC3SOFTWAREHIS A:105 , GLN A:119 , ASN A:122BINDING SITE FOR RESIDUE ACT A 211
04AC4SOFTWAREHOH A:304BINDING SITE FOR RESIDUE PGO A 212
05AC5SOFTWAREPHE A:74 , GLY A:77BINDING SITE FOR RESIDUE PGO A 216
06AC6SOFTWAREARG B:18 , ASP B:22 , HOH B:273 , HOH B:512 , HOH C:545 , HOH C:546BINDING SITE FOR RESIDUE ACT B 200
07AC7SOFTWAREASP B:6 , HOH B:502BINDING SITE FOR RESIDUE ACT B 202
08AC8SOFTWAREPHE B:74 , GLY B:77 , ASP B:79 , HOH B:562BINDING SITE FOR RESIDUE ACT B 203
09AC9SOFTWAREPHE B:102 , ARG B:103 , TYR B:159 , GLN B:163BINDING SITE FOR RESIDUE ACT B 206
10BC1SOFTWARETRP B:185 , THR B:194 , HOH B:226 , HOH B:543BINDING SITE FOR RESIDUE PGO B 213
11BC2SOFTWAREGLN B:65 , ARG B:98BINDING SITE FOR RESIDUE PGO B 215
12BC3SOFTWAREPRO C:99 , ARG C:103 , TYR C:159 , GLN C:163BINDING SITE FOR RESIDUE ACT C 204
13BC4SOFTWAREHIS C:105 , THR C:109 , GLN C:119 , ASN C:122BINDING SITE FOR RESIDUE ACT C 210
14BC5SOFTWAREARG D:98BINDING SITE FOR RESIDUE ACT D 207
15BC6SOFTWAREGLU D:14 , ARG D:98 , GLU D:100 , HOH D:624BINDING SITE FOR RESIDUE ACT D 208
16BC7SOFTWAREARG B:85 , HIS B:89 , HOH B:281 , ILE D:46BINDING SITE FOR RESIDUE ACT D 209
17BC8SOFTWAREARG D:121 , SER D:124 , ARG D:125 , HOH D:670BINDING SITE FOR RESIDUE PGO D 214

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PAS)

(-) 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:191
 aligned with A1U0I5_MARHV | A1U0I5 from UniProtKB/TrEMBL  Length:194

    Alignment length:191
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190 
         A1U0I5_MARHV     1 MRQRDDSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFRIGLERPELFRYHETFTHSAWMTPEIQARNESRAANLLNAVDQGKQSGLIKPVPFPLLETFMFRPIYHLVQRCLQGSFEGTDEHIELAFNMAWDAVADR 191
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pas A   1 mRQRDDSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFRIGLERPELFRYHETFTHSAWmTPEIQARNESRAANLLNAVDQGKQSGLIKPVPFPLLETFmFRPIYHLVQRCLQGSFEGTDEHIELAFNmAWDAVADR 191
                            |       10        20        30        40        50        60        70        80        90       100       110   |   120       130       140       150   |   160       170       180  |    190 
                            |                                                                                                              114-MSE                                 154-MSE                      183-MSE    
                            1-MSE                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:192
 aligned with A1U0I5_MARHV | A1U0I5 from UniProtKB/TrEMBL  Length:194

    Alignment length:192
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192  
         A1U0I5_MARHV     3 QRDDSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFRIGLERPELFRYHETFTHSAWMTPEIQARNESRAANLLNAVDQGKQSGLIKPVPFPLLETFMFRPIYHLVQRCLQGSFEGTDEHIELAFNMAWDAVADRRNT 194
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pas B   3 QRDDSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFRIGLERPELFRYHETFTHSAWmTPEIQARNESRAANLLNAVDQGKQSGLIKPVPFPLLETFmFRPIYHLVQRCLQGSFEGTDEHIELAFNmAWDAVADRRNT 194
                                    12        22        32        42        52        62        72        82        92       102       112 |     122       132       142       152 |     162       172       182|      192  
                                                                                                                                         114-MSE                                 154-MSE                      183-MSE       


Chain C from PDB  Type:PROTEIN  Length:192
 aligned with A1U0I5_MARHV | A1U0I5 from UniProtKB/TrEMBL  Length:194

    Alignment length:192
                             1                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189  
         A1U0I5_MARHV     - -MRQRDDSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFRIGLERPELFRYHETFTHSAWMTPEIQARNESRAANLLNAVDQGKQSGLIKPVPFPLLETFMFRPIYHLVQRCLQGSFEGTDEHIELAFNMAWDAVADR 191
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pas C   0 GmRQRDDSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFRIGLERPELFRYHETFTHSAWmTPEIQARNESRAANLLNAVDQGKQSGLIKPVPFPLLETFmFRPIYHLVQRCLQGSFEGTDEHIELAFNmAWDAVADR 191
                             |       9        19        29        39        49        59        69        79        89        99       109    |  119       129       139       149    |  159       169       179   |   189  
                             1-MSE                                                                                                          114-MSE                                 154-MSE                      183-MSE    


Chain D from PDB  Type:PROTEIN  Length:192
 aligned with A1U0I5_MARHV | A1U0I5 from UniProtKB/TrEMBL  Length:194

    Alignment length:192
                             1                                                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189  
         A1U0I5_MARHV     - -MRQRDDSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFRIGLERPELFRYHETFTHSAWMTPEIQARNESRAANLLNAVDQGKQSGLIKPVPFPLLETFMFRPIYHLVQRCLQGSFEGTDEHIELAFNMAWDAVADR 191
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pas D   0 GmRQRDDSKRIAFLEATVREVADHGFSATSVGKIAKAAGLSPATLYIYYEDKEQLLLATFYYVSDQVIDAALDSFSRGKDLREGLRRQWHTLFRIGLERPELFRYHETFTHSAWmTPEIQARNESRAANLLNAVDQGKQSGLIKPVPFPLLETFmFRPIYHLVQRCLQGSFEGTDEHIELAFNmAWDAVADR 191
                             |       9        19        29        39        49        59        69        79        89        99       109    |  119       129       139       149    |  159       169       179   |   189  
                             1-MSE                                                                                                          114-MSE                                 154-MSE                      183-MSE
   Legend:   → Mismatch (orange background)
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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 3PAS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A1U0I5_MARHV | A1U0I5)
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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