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(-) Description

Title :  THE CRYSTAL STRUCTURE OF POSSIBLE TRANSCRIPTIONAL REGULATOR YYDK FROM BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
 
Authors :  K. Tan, M. Zhou, J. Abdullah, A. Joachimiak, Midwest Center For Stru Genomics (Mcsg)
Date :  09 Jan 08  (Deposition) - 22 Jan 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Keywords :  Apc85486, Yydk, Transcriptional Regulator, Structural Genomics, Psi- 2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Dna-Binding, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, M. Zhou, J. Abdullah, A. Joachimiak
The Crystal Structure Of Possible Transcriptional Regulator Yydk From Bacillus Subtilis Subsp. Subtilis Str. 168.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UNCHARACTERIZED HTH-TYPE TRANSCRIPTIONAL REGULATOR YYDK
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: YYDK, BSU40130
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Strain: 168

 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  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:93 , TYR A:128 , GLU B:17BINDING SITE FOR RESIDUE EDO A 237
02AC2SOFTWARELYS A:198 , LEU A:199 , TYR A:220 , TYR A:222 , SER A:225 , PHE A:227 , VAL B:179BINDING SITE FOR RESIDUE EDO A 238
03AC3SOFTWAREGLN A:21 , GLN A:22 , LYS A:68 , LYS A:70BINDING SITE FOR RESIDUE EDO A 239
04AC4SOFTWARETYR A:136 , GLU A:138 , GLU A:186 , TYR A:200 , LYS A:217 , SER A:219 , HOH A:322BINDING SITE FOR RESIDUE EDO A 240
05AC5SOFTWAREARG B:71 , LYS B:72 , ALA C:109 , ASN C:113 , ILE C:114BINDING SITE FOR RESIDUE EDO C 237
06AC6SOFTWARETYR C:136 , GLU C:138 , GLU C:186 , LYS C:217 , SER C:219 , HOH C:318BINDING SITE FOR RESIDUE EDO C 238
07AC7SOFTWARETYR B:136 , GLU B:138 , GLU B:186 , LYS B:217 , SER B:219BINDING SITE FOR RESIDUE EDO B 237
08AC8SOFTWARELEU C:112 , ASN C:113 , GLN C:211 , PRO C:212 , HOH C:260BINDING SITE FOR RESIDUE EDO C 239
09AC9SOFTWAREVAL A:179 , LYS B:198 , LEU B:199 , TYR B:220 , TYR B:222 , SER B:225 , PHE B:227 , HOH B:246BINDING SITE FOR RESIDUE EDO B 238
10BC1SOFTWARELYS C:198 , LEU C:199 , TYR C:220 , ASN C:221 , TYR C:222 , SER C:225 , HOH C:270BINDING SITE FOR RESIDUE EDO C 240

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_GNTRPS50949 GntR-type HTH domain profile.YYDK_BACSU1-69  1B:1-69
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_GNTRPS50949 GntR-type HTH domain profile.YYDK_BACSU1-69  1B:1-69
Biological Unit 2 (, 0)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_GNTRPS50949 GntR-type HTH domain profile.YYDK_BACSU1-69  0-

(-) Exons   (0, 0)

(no "Exon" information available for 3BWG)

(-) 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:223
 aligned with YYDK_BACSU | Q45591 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:229
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224         
           YYDK_BACSU     5 QQIATEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVRGSGIFVRKHKRKGYISLLSNQGFKKDLEDFNVTSKVIELDVRKPTPEAAENLNIGMDEDIYYVKRVRYINGQTLCYEESYYTKSIVTYLNNEIVSHSIFHYIREGLGLKIGFSDLFLHVGQLNEEEAEYLGLEAGLPKLYIESIFHLTNGQPFDYSKISYNYEQSQFVVQANS 233
               SCOP domains d3bwga1 A:5-82 Transcriptional regulator YydK                                 ------d3bwga2 A:89-233 Transcriptional regulator YydK                                                                                                   SCOP domains
               CATH domains 3bwgA01 A:5-70 'winged helix' repressor DNA binding domain        3bwgA02 A:71      -233 Chorismate lyase                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.........hhhhhhhhh..hhhhhhhhhhhhhhh..eeee...eeee........ee.hhhhh------...eeeeeeeeeee..hhhhhhhhh......eeeeeeeeee..eeeeeeeeeee.......hhhhhh.hhhhhhhhh....eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee....eeeeeeeee......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_GNTR  PDB: - UniProt: 1-69                                   -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwg A   5 QQIATEIETYIEEHQLQQGDKLPVLETLmAQFEVSKSTITKSLELLEQKGAIFQVRGSGIFVRKHKRKGYISLLSNQG------DFNVTSKVIELDVRKPTPEAAENLNIGmDEDIYYVKRVRYINGQTLCYEESYYTKSIVTYLNNEIVSHSIFHYIREGLGLKIGFSDLFLHVGQLNEEEAEYLGLEAGLPKLYIESIFHLTNGQPFDYSKISYNYEQSQFVVQANS 233
                                    14        24        34        44        54        64        74       | -    |   94       104       114 |     124       134       144       154       164       174       184       194       204       214       224         
                                                       33-MSE                                           82     89                        116-MSE                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with YYDK_BACSU | Q45591 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:232
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230  
           YYDK_BACSU     1 MLKYQQIATEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVRGSGIFVRKHKRKGYISLLSNQGFKKDLEDFNVTSKVIELDVRKPTPEAAENLNIGMDEDIYYVKRVRYINGQTLCYEESYYTKSIVTYLNNEIVSHSIFHYIREGLGLKIGFSDLFLHVGQLNEEEAEYLGLEAGLPKLYIESIFHLTNGQPFDYSKISYNYEQSQFVVQAN 232
               SCOP domains d3bwgb1 B:1-81 Transcriptional regulator YydK                                    -------d3bwgb2 B:89-232 Transcriptional regulator YydK                                                                                                  SCOP domains
               CATH domains -3bwgB01 B:2-70 'winged helix' repressor DNA binding domain           3bwgB02 B:7    1-232 Chorismate lyase                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee........ee.....----hhhhh.eeeeeeeeeee..hhhhhhhh.......eeeeeeeeee..eeeeeeeeeee.......hhhhhh.hhhhhhhhh....eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee....eeeeeeeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_GNTR  PDB: B:1-69 UniProt: 1-69                                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwg B   1 mLKYQQIATEIETYIEEHQLQQGDKLPVLETLmAQFEVSKSTITKSLELLEQKGAIFQVRGSGIFVRKHKRKGYISLLSNQ----DLEDFNVTSKVIELDVRKPTPEAAENLNIGmDEDIYYVKRVRYINGQTLCYEESYYTKSIVTYLNNEIVSHSIFHYIREGLGLKIGFSDLFLHVGQLNEEEAEYLGLEAGLPKLYIESIFHLTNGQPFDYSKISYNYEQSQFVVQAN 232
                            |       10        20        30  |     40        50        60        70        80|    |  90       100       110     | 120       130       140       150       160       170       180       190       200       210       220       230  
                            1-MSE                          33-MSE                                          81   86                           116-MSE                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:224
 aligned with YYDK_BACSU | Q45591 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:231
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232 
           YYDK_BACSU     3 KYQQIATEIETYIEEHQLQQGDKLPVLETLMAQFEVSKSTITKSLELLEQKGAIFQVRGSGIFVRKHKRKGYISLLSNQGFKKDLEDFNVTSKVIELDVRKPTPEAAENLNIGMDEDIYYVKRVRYINGQTLCYEESYYTKSIVTYLNNEIVSHSIFHYIREGLGLKIGFSDLFLHVGQLNEEEAEYLGLEAGLPKLYIESIFHLTNGQPFDYSKISYNYEQSQFVVQANS 233
               SCOP domains d3bwgc1 C:3-79 Transcriptional regulator YydK                                ---------d3bwgc2 C:89-233 Transcriptional regulator YydK                                                                                                   SCOP domains
               CATH domains 3bwgC01 C:3-70 'winged helix' repressor DNA binding domain          3bwgC02 C       :71-233 Chorismate lyase                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee........ee...-------.....eeeeeeeeeee..hhhhhhhhh......eeeeeeeeee..eeeeeeeeeee.......hhhhhh.hhhhhhhhh....eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee....eeeeeeeee......ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE HTH_GNTR  PDB: - UniProt: 1-69                                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bwg C   3 KYQQIATEIETYIEEHQLQQGDKLPVLETLmAQFEVSKSTITKSLELLEQKGAIFQVRGSGIFVRKHKRKGYISLLS-------LEDFNVTSKVIELDVRKPTPEAAENLNIGmDEDIYYVKRVRYINGQTLCYEESYYTKSIVTYLNNEIVSHSIFHYIREGLGLKIGFSDLFLHVGQLNEEEAEYLGLEAGLPKLYIESIFHLTNGQPFDYSKISYNYEQSQFVVQANS 233
                                    12        22        32|       42        52        62        72      |  -    |   92       102       112   |   122       132       142       152       162       172       182       192       202       212       222       232 
                                                         33-MSE                                        79      87                          116-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (2, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (YYDK_BACSU | Q45591)
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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  3bwg
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  YYDK_BACSU | Q45591
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