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(-) Description

Title :  CRYSTAL STRUCTURE OF THE TRANSCRIPTION REGULATOR MARR FROM OENOCOCCUS OENI PSU-1
 
Authors :  Y. Kim, L. Volkart, M. Gu, A. Joachimiak, Midwest Center For Structu Genomics (Mcsg)
Date :  21 Dec 07  (Deposition) - 15 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Helix_turn_helix, Multiple Antibiotic Resistance Protein (Marr), Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, L. Volkart, M. Gu, A. Joachimiak
Crystal Structure Of The Transcription Regulator Marr From Oenococcus Oeni Psu-1.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Atcc: BAA-331
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: OEOE_1854
    Organism Scientific: OENOCOCCUS OENI
    Organism Taxid: 203123
    Strain: PSU-1

 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, 28)

Asymmetric Unit (3, 28)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE25Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 13)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL-1Ligand/IonGLYCEROL
3MSE13Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 13)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:93 , HOH A:272 , HOH A:386BINDING SITE FOR RESIDUE CL A 201
2AC2SOFTWAREARG A:42 , ASN A:43 , ARG B:7BINDING SITE FOR RESIDUE CL A 202
3AC3SOFTWAREGLY C:6 , MSE D:16 , PHE D:20 , MSE D:108 , ASP D:111 , GLN D:112 , HOH D:272BINDING SITE FOR RESIDUE GOL D 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BRO)

(-) 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:135
 aligned with Q04CY6_OENOB | Q04CY6 from UniProtKB/TrEMBL  Length:138

    Alignment length:135
                                    12        22        32        42        52        62        72        82        92       102       112       122       132     
         Q04CY6_OENOB     3 RDLGRLLKIASNQMSTRFDIFAKKYDLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYMDSDQSQMTSGLNKEEVVFLEKILKRMIES 137
               SCOP domains d3broa1 A:3-137 Transcriptional regulator OEOE1854                                                                                      SCOP domains
               CATH domains 3broA00 A:3-137 'winged helix' repressor DNA binding domain                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bro A   3 RDLGRLLKIASNQmSTRFDIFAKKYDLTGTQmTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRmEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYmDSDQSQmTSGLNKEEVVFLEKILKRmIES 137
                                    12   |    22        32 |      42        52        62        72        82        92       102     | 112  |    122       132 |   
                                        16-MSE            34-MSE                               71-MSE                              108-MSE  |                134-MSE
                                                                                                                                          115-MSE                  


Chain B from PDB  Type:PROTEIN  Length:140
 aligned with Q04CY6_OENOB | Q04CY6 from UniProtKB/TrEMBL  Length:138

    Alignment length:140
                              1                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138
         Q04CY6_OENOB     - --MSRDLGRLLKIASNQMSTRFDIFAKKYDLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYMDSDQSQMTSGLNKEEVVFLEKILKRMIESD 138
               SCOP domains d3brob_ B: Transcriptional regulator OEOE1854                                                                                                SCOP domains
               CATH domains 3broB00 B:-1-138 'winged helix' repressor DNA binding domain                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bro B  -1 NAmSRDLGRLLKIASNQmSTRFDIFAKKYDLTGTQmTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRmEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYmDSDQSQmTSGLNKEEVVFLEKILKRmIESD 138
                              |      8       |18        28     |  38        48        58        68  |     78        88        98       108      |118       128     | 138
                              1-MSE         16-MSE            34-MSE                               71-MSE                              108-MSE  |                134-MSE
                                                                                                                                              115-MSE                   


Chain C from PDB  Type:PROTEIN  Length:135
 aligned with Q04CY6_OENOB | Q04CY6 from UniProtKB/TrEMBL  Length:138

    Alignment length:135
                                    13        23        33        43        53        63        73        83        93       103       113       123       133     
         Q04CY6_OENOB     4 DLGRLLKIASNQMSTRFDIFAKKYDLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYMDSDQSQMTSGLNKEEVVFLEKILKRMIESD 138
               SCOP domains d3broc_ C: Transcriptional regulator OEOE1854                                                                                           SCOP domains
               CATH domains 3broC00 C:4-138 'winged helix' repressor DNA binding domain                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bro C   4 DLGRLLKIASNQmSTRFDIFAKKYDLTGTQmTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRmEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYmDSDQSQmTSGLNKEEVVFLEKILKRmIESD 138
                                    13  |     23        33|       43        53        63       |73        83        93       103    |  113 |     123       133|    
                                       16-MSE            34-MSE                               71-MSE                              108-MSE  |                134-MSE
                                                                                                                                         115-MSE                   


Chain D from PDB  Type:PROTEIN  Length:134
 aligned with Q04CY6_OENOB | Q04CY6 from UniProtKB/TrEMBL  Length:138

    Alignment length:134
                                    13        23        33        43        53        63        73        83        93       103       113       123       133    
         Q04CY6_OENOB     4 DLGRLLKIASNQMSTRFDIFAKKYDLTGTQMTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRMEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYMDSDQSQMTSGLNKEEVVFLEKILKRMIES 137
               SCOP domains d3brod_ D: Transcriptional regulator OEOE1854                                                                                          SCOP domains
               CATH domains 3broD00 D:4-137 'winged helix' repressor DNA binding domain                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bro D   4 DLGRLLKIASNQmSTRFDIFAKKYDLTGTQmTIIDYLSRNKNKEVLQRDLESEFSIKSSTATVLLQRmEIKKLLYRKVSGKDSRQKCLKLTKKANKLETIILSYmDSDQSQmTSGLNKEEVVFLEKILKRmIES 137
                                    13  |     23        33|       43        53        63       |73        83        93       103    |  113 |     123       133|   
                                       16-MSE            34-MSE                               71-MSE                              108-MSE  |                134-MSE
                                                                                                                                         115-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  (1, 4)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q04CY6_OENOB | Q04CY6)
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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