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(-) Description

Title :  CRYSTAL STRUCTURE OF A LACI FAMILY TRANSCRIPTIONAL REGULATOR FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  J. B. Bonanno, M. Rutter, K. T. Bain, J. Do, S. Ozyurt, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  05 Nov 09  (Deposition) - 08 Dec 09  (Release) - 08 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Structural Genomics, Transcription, Dna-Binding, Transcription Regulation, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, M. Rutter, K. T. Bain, J. Do, S. Ozyurt, S. Wasserman, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Laci Family Transcriptional Regulator From Mycobacterium Smegmatis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LACI FAMILY TRANSCRIPTIONAL REGULATOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MSMEG_0491
    Organism Scientific: MYCOBACTERIUM SMEGMATIS STR. MC2 155
    Organism Taxid: 246196
    Strain: ATCC 700084 / MC(2)155

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:75 , ASN A:147 , ARG A:195 , TRP A:220 , SER A:251 , ASN A:279BINDING SITE FOR RESIDUE ACT A 1
2AC2SOFTWAREVAL A:287 , TYR A:288 , HOH A:535 , SER D:260 , VAL D:287 , TYR D:288BINDING SITE FOR RESIDUE ACT A 350
3AC3SOFTWAREVAL B:75 , ASN B:147 , ARG B:195 , TRP B:220 , SER B:251 , ASN B:279BINDING SITE FOR RESIDUE ACT B 1
4AC4SOFTWAREVAL C:75 , ASN C:147 , ARG C:195 , TRP C:220 , SER C:251 , ASN C:279BINDING SITE FOR RESIDUE ACT C 1
5AC5SOFTWAREVAL D:75 , ASN D:147 , ARG D:195 , TRP D:220 , SER D:251 , ASN D:279BINDING SITE FOR RESIDUE ACT D 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (16, 16)

Asymmetric Unit
No.Residues
1Pro A:102 -Pro A:103
2Val A:269 -Pro A:270
3Tyr A:288 -Pro A:289
4Gln A:325 -Pro A:326
5Pro B:102 -Pro B:103
6Val B:269 -Pro B:270
7Tyr B:288 -Pro B:289
8Gln B:325 -Pro B:326
9Pro C:102 -Pro C:103
10Val C:269 -Pro C:270
11Tyr C:288 -Pro C:289
12Gln C:325 -Pro C:326
13Pro D:102 -Pro D:103
14Val D:269 -Pro D:270
15Tyr D:288 -Pro D:289
16Gln D:325 -Pro D:326

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KKE)

(-) 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:278
 aligned with A0QPR6_MYCS2 | A0QPR6 from UniProtKB/TrEMBL  Length:342

    Alignment length:278
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        
         A0QPR6_MYCS2    63 TIGLIVPDVNNAVFADMFSGVQMAASGHSTDVLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLEGVPAVTINSRVPGRVGSVILDDQKGGGIATEHLITLGHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVASVNAAVGALSTALRLGLRVPEDLSIVGINTTWVSDTVYPALTTVRLPLQRLGEVAADVLMEHLGGRALTDTVVTQPTPELLVRETTAPPT 340
               SCOP domains d3kkea_ A: automated matches                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhh....eeee......hhhhhhhhhh...eeee.........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh....hhh.eee...hhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhhhh........eeeee..hhhhhhh....eeee.hhhhhhhhhhhhhhhhhh.....eeee.....eee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kke A  63 TIGLIVPDVNNAVFADMFSGVQMAASGHSTDVLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLEGVPAVTINSRVPGRVGSVILDDQKGGGIATEHLITLGHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVASVNAAVGALSTALRLGLRVPEDLSIVGINTTWVSDTVYPALTTVRLPLQRLGEVAADVLMEHLGGRALTDTVVTQPTPELLVRETTAPPT 340
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332        


Chain B from PDB  Type:PROTEIN  Length:291
 aligned with A0QPR6_MYCS2 | A0QPR6 from UniProtKB/TrEMBL  Length:342

    Alignment length:291
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339 
         A0QPR6_MYCS2    50 NARARALRHSRSGTIGLIVPDVNNAVFADMFSGVQMAASGHSTDVLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLEGVPAVTINSRVPGRVGSVILDDQKGGGIATEHLITLGHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVASVNAAVGALSTALRLGLRVPEDLSIVGINTTWVSDTVYPALTTVRLPLQRLGEVAADVLMEHLGGRALTDTVVTQPTPELLVRETTAPPT 340
               SCOP domains d3kkeb_ B: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh.....eee......hhhhhhhhhh...eeee.........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhh....hhh.eee...hhhhhhhhhhhhhhhhh........eeee.hhhhhhhhhhhhhhh........eeeee..hhhhhhh....eeee.hhhhhhhhhhhhhhhhhh.....eeee.....eee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kke B  50 NARARALRHSRSGTIGLIVPDVNNAVFADMFSGVQMAASGHSTDVLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLEGVPAVTINSRVPGRVGSVILDDQKGGGIATEHLITLGHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVASVNAAVGALSTALRLGLRVPEDLSIVGINTTWVSDTVYPALTTVRLPLQRLGEVAADVLMEHLGGRALTDTVVTQPTPELLVRETTAPPT 340
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339 


Chain C from PDB  Type:PROTEIN  Length:285
 aligned with A0QPR6_MYCS2 | A0QPR6 from UniProtKB/TrEMBL  Length:342

    Alignment length:285
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334     
         A0QPR6_MYCS2    55 ALRHSRSGTIGLIVPDVNNAVFADMFSGVQMAASGHSTDVLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLEGVPAVTINSRVPGRVGSVILDDQKGGGIATEHLITLGHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVASVNAAVGALSTALRLGLRVPEDLSIVGINTTWVSDTVYPALTTVRLPLQRLGEVAADVLMEHLGGRALTDTVVTQPTPELLVRETTAPP 339
               SCOP domains d3kkec_ C: automated matches                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.......hhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh....eeeee.....hhhhhhhhhh...eeee.........eeeehhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhh....hhh.ee....hhhhhhhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhh.......eeeee..hhhhhhh....eeee.hhhhhhhhhhhhhhhhh......eeee.....eee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kke C  55 ALRHSRSGTIGLIVPDVNNAVFADMFSGVQMAASGHSTDVLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLEGVPAVTINSRVPGRVGSVILDDQKGGGIATEHLITLGHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVASVNAAVGALSTALRLGLRVPEDLSIVGINTTWVSDTVYPALTTVRLPLQRLGEVAADVLMEHLGGRALTDTVVTQPTPELLVRETTAPP 339
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334     


Chain D from PDB  Type:PROTEIN  Length:277
 aligned with A0QPR6_MYCS2 | A0QPR6 from UniProtKB/TrEMBL  Length:342

    Alignment length:277
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       
         A0QPR6_MYCS2    63 TIGLIVPDVNNAVFADMFSGVQMAASGHSTDVLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLEGVPAVTINSRVPGRVGSVILDDQKGGGIATEHLITLGHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVASVNAAVGALSTALRLGLRVPEDLSIVGINTTWVSDTVYPALTTVRLPLQRLGEVAADVLMEHLGGRALTDTVVTQPTPELLVRETTAPP 339
               SCOP domains d3kked_ D: automated matches                                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------Peripla_BP_3-3kkeD01 D:169-336                                                                                                                                          --- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------Peripla_BP_3-3kkeD02 D:169-336                                                                                                                                          --- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------Peripla_BP_3-3kkeD03 D:169-336                                                                                                                                          --- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------Peripla_BP_3-3kkeD04 D:169-336                                                                                                                                          --- Pfam domains (4)
         Sec.struct. author .eeee.......hhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh....eeeee.....hhhhhhhhhh...eeee.........eeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhh.......eee...hhhhhhhhhhhhhhhh.........eeee.hhhhhhhhhhhhhhhh.......eeeee..hhhhhhh....eeee.hhhhhhhhhhhhhhhhhh.....eeee.....eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kke D  63 TIGLIVPDVNNAVFADMFSGVQMAASGHSTDVLLGQIDAPPRGTQQLSRLVSEGRVDGVLLQRREDFDDDMLAAVLEGVPAVTINSRVPGRVGSVILDDQKGGGIATEHLITLGHSRIAFISGTAIHDTAQRRKEGYLETLASAGLRSEAAWVVDAGWEADAGSAALNTLYRGANLGKPDGPTAVVVASVNAAVGALSTALRLGLRVPEDLSIVGINTTWVSDTVYPALTTVRLPLQRLGEVAADVLMEHLGGRALTDTVVTQPTPELLVRETTAPP 339
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332
   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Periplas_BP (97)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (A0QPR6_MYCS2 | A0QPR6)
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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