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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRANSCRIPTIONAL REGULATOR
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YERO
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1DCC1Ligand/IonDODECYL-COA
2MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:58 , LYS A:61 , MSE A:62 , GLU A:81 , HIS A:90 , LEU A:93 , THR A:104 , ARG A:109 , ARG A:116 , ASN A:120 , LYS A:124 , LEU A:127 , ARG A:150 , LEU A:151 , ARG A:153 , GLN A:154 , HOH A:226 , HOH A:245 , HOH A:250 , HOH A:257 , HOH A:266 , HOH A:280 , GLU B:162 , THR B:165 , THR B:166 , MSE B:169 , ASN B:170 , LYS B:173 , TYR B:174BINDING SITE FOR RESIDUE DCC A 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VI0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VI0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VI0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1VI0)

(-) Exons   (0, 0)

(no "Exon" information available for 1VI0)

(-) Sequences/Alignments

Asymmetric/Biological 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:189
 aligned with FADR_BACSU | P94548 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:189
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185         
           FADR_BACSU     6 PKYMQIIDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFKNKEDILISLFKEKMGQFIERMEEDIKEKATAKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEGIQSGEIKEGLDVRLARQMIFGTIDETVTTWVMNDQKYDLVALSNSVLELLVSGIHNK 194
               SCOP domains d1vi0a1 A:6-77 Hypothetical transcriptional regulator YsiA              d1vi0a2 A:78-194 Hypothetical transcriptional regulator YsiA                                                          SCOP domains
               CATH domains 1vi0A01 A:6-49 Homeodomain-like             1vi0A02 A:50-194 Tetracycline Repressor, domain 2                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi0 A   6 PKYmQIIDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFKNKEDILISLFKEKmGQFIERmEEDIKEKATAKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEGIQSGEIKEGLDVRLARQmIFGTIDETVTTWVmNDQKYDLVALSNSVLELLVSGIHNK 194
                               |    15        25        35        45        55      | 65   |    75        85        95       105       115       125       135       145       155       165   |   175       185         
                               |                                                   62-MSE 69-MSE                                                                               155-MSE       169-MSE                     
                               9-MSE                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with FADR_BACSU | P94548 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:188
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185        
           FADR_BACSU     6 PKYMQIIDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFKNKEDILISLFKEKMGQFIERMEEDIKEKATAKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEGIQSGEIKEGLDVRLARQMIFGTIDETVTTWVMNDQKYDLVALSNSVLELLVSGIHN 193
               SCOP domains d1vi0b1 B:6-77 Hypothetical transcriptional regulator YsiA              d1vi0b2 B:78-193 Hypothetical transcriptional regulator YsiA                                                         SCOP domains
               CATH domains 1vi0B01 B:6-49 Homeodomain-like             1vi0B02 B:50-193 Tetracycline Repressor, domain 2                                                                                                CATH domains
           Pfam domains (1) -----TetR_N-1vi0B01 B:11-57                         TetR_C_4-1vi0B03 B:58-190                                                                                                            --- Pfam domains (1)
           Pfam domains (2) -----TetR_N-1vi0B02 B:11-57                         TetR_C_4-1vi0B04 B:58-190                                                                                                            --- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vi0 B   6 PKYmQIIDAAVEVIAENGYHQSQVSKIAKQAGVADGTIYLYFKNKEDILISLFKEKmGQFIERmEEDIKEKATAKEKLALVISKHFSLLAGDHNLAIVTQLELRQSNLELRQKINEILKGYLNILDGILTEGIQSGEIKEGLDVRLARQmIFGTIDETVTTWVmNDQKYDLVALSNSVLELLVSGIHN 193
                               |    15        25        35        45        55      | 65   |    75        85        95       105       115       125       135       145       155       165   |   175       185        
                               9-MSE                                               62-MSE 69-MSE                                                                               155-MSE       169-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  (2, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: TetR_C (33)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FADR_BACSU | P94548)
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:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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        FADR_BACSU | P94548: 3whb 3whc

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