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(-) Description

Title :  CRYSTAL STRUCTURE OF SCO4454, A TETR-FAMILY TRANSCRIPTIONAL REGULATOR FROM STREPTOMYCES COELICOLOR
 
Authors :  A. U. Singer, X. Xu, C. Chang, J. Gu, A. M. Edwards, A. Joachimiak, A. Savchenko, Midwest Center For Structural Genomics (Mcsg)
Date :  10 Feb 09  (Deposition) - 10 Mar 09  (Release) - 10 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.38
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tetr, Transcriptional Regulator, Streptomyces Coelicolor, All-Helical, 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 :  A. U. Singer, X. Xu, C. Chang, A. M. Edwards, A. Joachimiak, A. Savchenko
Structure And Ligand Specificity Of Sco4454, A Tetr-Family Transcriptional Regulator From Streptomyces Coelicolor
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE TRANSCRIPTIONAL REGULATOR
    Atcc: BAA-471
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TVLIC
    Expression System Strain: BL21(DE3) CODON PLUS RIPL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SCD6.32C, SCO4454
    Organism Scientific: STREPTOMYCES COELICOLOR A3(2)
    Organism Taxid: 100226
    Strain: A3(2) / M145

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 42)

Asymmetric/Biological Unit (6, 42)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO27Ligand/Ion1,2-ETHANEDIOL
3IOD3Ligand/IonIODIDE ION
4MSE5Mod. Amino AcidSELENOMETHIONINE
5NA2Ligand/IonSODIUM ION
6PEG2Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:73 , HIS A:133 , PHE A:137 , ARG A:164 , HOH A:618 , HOH A:955 , HOH A:1022BINDING SITE FOR RESIDUE EDO A 960
02AC2SOFTWAREALA A:75 , ALA A:79 , HOH A:304 , HOH A:344BINDING SITE FOR RESIDUE EDO A 962
03AC3SOFTWAREARG A:103 , GLU A:177 , HOH A:225 , HOH A:264 , EDO B:973BINDING SITE FOR RESIDUE EDO A 963
04AC4SOFTWAREALA A:17 , ARG A:18 , THR A:22 , HOH A:427BINDING SITE FOR RESIDUE EDO A 965
05AC5SOFTWAREALA A:155 , GLU B:181 , THR B:182 , HOH B:308BINDING SITE FOR RESIDUE EDO A 966
06AC6SOFTWARELEU A:145 , ALA A:146 , GLY A:149 , GLY A:151 , ASP A:152 , GLY A:153 , VAL A:194 , HOH A:247 , HOH A:368 , HOH A:648BINDING SITE FOR RESIDUE EDO A 967
07AC7SOFTWAREASP A:88 , ARG A:92 , LEU A:191 , SER A:195 , HOH A:334 , HOH A:382 , ARG B:53 , HOH B:381BINDING SITE FOR RESIDUE EDO A 969
08AC8SOFTWAREGLN A:90 , HOH A:234 , HOH A:259 , HOH A:300 , HOH A:637 , HOH A:943 , ARG B:48BINDING SITE FOR RESIDUE EDO A 971
09AC9SOFTWARESER A:13 , ARG A:53 , HOH A:908 , VAL B:148 , SER B:195 , HOH B:276BINDING SITE FOR RESIDUE EDO A 979
10BC1SOFTWARETHR A:78 , HOH A:376 , HOH A:392 , EDO A:988BINDING SITE FOR RESIDUE EDO A 980
11BC2SOFTWARETRP A:136 , ASP A:139 , THR A:140 , HOH A:351 , HOH A:649 , HOH A:651 , HOH A:662 , HOH A:974BINDING SITE FOR RESIDUE EDO A 982
12BC3SOFTWAREVAL A:148 , GLY A:149 , SER A:195 , HOH A:657 , HOH A:1027 , SER B:13 , ARG B:53 , HIS B:54 , HOH B:330BINDING SITE FOR RESIDUE EDO A 983
13BC4SOFTWAREALA A:29 , HOH A:273 , HOH A:1012 , ASP B:121BINDING SITE FOR RESIDUE EDO A 984
14BC5SOFTWAREALA A:146 , GLY A:149 , ASP A:150 , GLY A:151 , ASP A:152 , HOH A:451 , HOH A:939 , HOH B:552 , EDO B:973BINDING SITE FOR RESIDUE EDO A 986
15BC6SOFTWAREARG A:74 , THR A:78 , TRP A:136 , HOH A:512 , HOH A:615 , EDO A:980BINDING SITE FOR RESIDUE EDO A 988
16BC7SOFTWAREASP A:59 , LEU A:63 , HIS A:124 , PRO A:125 , HOH A:367 , HOH A:672 , HOH A:853 , HOH B:598BINDING SITE FOR RESIDUE PEG A 201
17BC8SOFTWARETYR A:119 , ASP A:121 , HOH A:789 , HOH A:862BINDING SITE FOR RESIDUE NA A 202
18BC9SOFTWAREGLN A:76 , SER A:97BINDING SITE FOR RESIDUE IOD A 203
19CC1SOFTWAREHIS B:133 , PHE B:137 , ARG B:164 , HOH B:218 , HOH B:600 , HOH B:946BINDING SITE FOR RESIDUE EDO B 961
20CC2SOFTWAREARG A:48 , ARG B:74 , TRP B:136 , HOH B:273 , HOH B:371BINDING SITE FOR RESIDUE EDO B 964
21CC3SOFTWAREGLU B:30 , SER B:34 , VAL B:35 , ARG B:39 , ARG B:128 , HOH B:311 , HOH B:400 , HOH B:790BINDING SITE FOR RESIDUE EDO B 970
22CC4SOFTWARELEU B:145 , ALA B:146 , GLY B:149 , GLY B:151 , ASP B:152 , GLY B:153 , VAL B:194 , HOH B:286 , HOH B:343 , HOH B:902BINDING SITE FOR RESIDUE EDO B 972
23CC5SOFTWAREARG A:103 , GLU A:143 , ALA A:146 , GLN A:147 , HOH A:915 , EDO A:963 , EDO A:986 , THR B:47 , HOH B:247BINDING SITE FOR RESIDUE EDO B 973
24CC6SOFTWARECL B:205 , HOH B:388 , EDO B:981BINDING SITE FOR RESIDUE EDO B 976
25CC7SOFTWAREARG A:53 , ASP B:88 , ARG B:92 , LEU B:191 , SER B:195 , HOH B:293 , HOH B:353BINDING SITE FOR RESIDUE EDO B 977
26CC8SOFTWAREASP B:38 , ARG B:48 , GLN B:135 , HOH B:627 , HOH B:881 , HOH B:897BINDING SITE FOR RESIDUE EDO B 978
27CC9SOFTWAREALA A:49 , HOH A:319 , HOH A:347 , ARG B:81 , GLN B:90 , HOH B:225 , HOH B:392 , HOH B:629 , EDO B:976BINDING SITE FOR RESIDUE EDO B 981
28DC1SOFTWAREPHE B:-2 , GLN B:-1 , PRO B:3 , SER B:4 , GLN B:68BINDING SITE FOR RESIDUE EDO B 985
29DC2SOFTWARELEU A:131 , LEU B:173 , HOH B:295 , HOH B:382 , HOH B:1013BINDING SITE FOR RESIDUE EDO B 987
30DC3SOFTWAREARG B:18 , GLY B:21 , THR B:22 , ARG B:25 , HOH B:673 , HOH B:969BINDING SITE FOR RESIDUE EDO B 989
31DC4SOFTWAREHOH A:791 , HIS B:33 , TYR B:119 , PRO B:120 , ASP B:121 , HIS B:124 , HOH B:294 , HOH B:452BINDING SITE FOR RESIDUE PEG B 201
32DC5SOFTWAREILE B:73 , GLN B:76 , SER B:97BINDING SITE FOR RESIDUE CL B 202
33DC6SOFTWARESER B:56 , GLY B:57BINDING SITE FOR RESIDUE CL B 203
34DC7SOFTWAREPHE B:174 , ASP B:175 , HOH B:216 , HOH B:691BINDING SITE FOR RESIDUE NA B 204
35DC8SOFTWAREARG A:48 , PRO B:85 , HOH B:221 , HOH B:629 , EDO B:976BINDING SITE FOR RESIDUE CL B 205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3G7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3G7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3G7R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3G7R)

(-) Exons   (0, 0)

(no "Exon" information available for 3G7R)

(-) 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 Q9KZX2_STRCO | Q9KZX2 from UniProtKB/TrEMBL  Length:200

    Alignment length:189
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187         
         Q9KZX2_STRCO     8 AARTPSEARARLLGTATRIFYAEGIHSVGIDRITAEAQVTRATLYRHFSGKDDLILAYLDQADRGIRAQVTAARGSSPAADGQVRAVARSIVDGIRSPGFRGCAFLNAVAEYPDPAHPVHRAVLAHRQWFLDTVTELLAQVGDGDGVAAGRHLVMLRDGAMAAGCLFDPELVSETFLHGVEGVLRDVSE 196
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g7rA00 A:-6-196 Tetracycline Repressor, domain 2                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh......hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g7r A  -6 NLYFQSEARARLLGTATRIFYAEGIHSVGIDRITAEAQVTRATLYRHFSGKDDLILAYLDQADRGIRAQVTAARGSSPAADGQVRAVARSIVDGIRSPGFRGCAFLNAVAEYPDPAHPVHRAVLAHRQWFLDTVTELLAQVGDGDGVAAGRHLVmLRDGAmAAGCLFDPELVSETFLHGVEGVLRDVSE 196
                                ||  17        27        37        47        57        67        77        87        97       107       117       127       137       147       157    |  167|      177       187         
                               -2|                                                                                                                                                  162-MSE |                            
                                13                                                                                                                                                        168-MSE                        


Chain B from PDB  Type:PROTEIN  Length:202
 aligned with Q9KZX2_STRCO | Q9KZX2 from UniProtKB/TrEMBL  Length:200

    Alignment length:202
                                  1                                                                                                                                                                                                   
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  
         Q9KZX2_STRCO     - ------MSPSTEAAARTPSEARARLLGTATRIFYAEGIHSVGIDRITAEAQVTRATLYRHFSGKDDLILAYLDQADRGIRAQVTAARGSSPAADGQVRAVARSIVDGIRSPGFRGCAFLNAVAEYPDPAHPVHRAVLAHRQWFLDTVTELLAQVGDGDGVAAGRHLVMLRDGAMAAGCLFDPELVSETFLHGVEGVLRDVSE 196
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3g7rB00 B:-5-196 Tetracycline Repressor, domain 2                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g7r B  -5 NLYFQGmSPSTEAAARTPSEARARLLGTATRIFYAEGIHSVGIDRITAEAQVTRATLYRHFSGKDDLILAYLDQADRGIRAQVTAARGSSPAADGQVRAVARSIVDGIRSPGFRGCAFLNAVAEYPDPAHPVHRAVLAHRQWFLDTVTELLAQVGDGDGVAAGRHLVmLRDGAmAAGCLFDPELVSETFLHGVEGVLRDVSE 196
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164   |   174       184       194  
                                  1-MSE                                                                                                                                                          162-MSE |                            
                                                                                                                                                                                                       168-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 3G7R)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3G7R)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9KZX2_STRCO | Q9KZX2)
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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