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(-) Description

Title :  CRYSTAL STRUCTURE OF RV1404 FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  M. Yu, E. H. Bursey, R. Radhakannan, C. -Y. Kim, T. Kaviratne, T. Woodruf B. W. Segelke, T. Lekin, D. Toppani, T. C. Terwilliger, L. -W. Hung, Tb Structural Genomics Consortium (Tbsgc), Integrated Center Fo Structure And Function Innovation (Isfi)
Date :  21 Nov 06  (Deposition) - 05 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alpha/Beta, Structural Genomics, Psi-2, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Integrated Center For Structure And Function Innovation, Isfi, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Yu, E. H. Bursey, R. Radhakannan, C. -Y. Kim, T. Kaviratne, T. Woodruff, B. W. Segelke, T. Lekin, D. Toppani, T. C. Terwilliger, L. -W. Hung
Crystal Structure Of Rv1404 From Mycobacterium Tuberculosis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN, RV1404
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RV1404
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 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  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2NYX)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NYX)

(-) Cis Peptide Bonds  (37, 37)

Asymmetric Unit
No.Residues
1Pro A:7 -Ala A:8
2Ala A:8 -Thr A:9
3Thr A:9 -Ala A:10
4Ala A:10 -Glu A:11
5Pro A:95 -Thr A:96
6Arg A:98 -Arg A:99
7Arg A:99 -Glu A:100
8Glu A:100 -Leu A:101
9Gly A:150 -Gly A:151
10Gly A:151 -Glu A:152
11Ala B:10 -Glu B:11
12Glu B:11 -Glu B:12
13Glu B:12 -Ser B:13
14Ser B:13 -Val B:14
15Val B:14 -Asp B:15
16Arg B:98 -Arg B:99
17Ala B:155 -Arg B:156
18Pro C:7 -Ala C:8
19Ala C:8 -Thr C:9
20Thr C:9 -Ala C:10
21Ala C:10 -Glu C:11
22Val C:71 -Gln C:72
23Gln C:72 -Pro C:73
24Pro C:95 -Thr C:96
25Gly C:151 -Glu C:152
26Ala D:10 -Glu D:11
27Glu D:11 -Glu D:12
28Glu D:12 -Ser D:13
29Pro D:93 -His D:94
30His D:94 -Pro D:95
31Pro D:95 -Thr D:96
32Thr D:96 -Ser D:97
33Ser D:97 -Arg D:98
34Arg D:98 -Arg D:99
35Arg D:99 -Glu D:100
36Glu D:100 -Leu D:101
37Ala D:155 -Arg D:156

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NYX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NYX)

(-) Exons   (0, 0)

(no "Exon" information available for 2NYX)

(-) 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:146
 aligned with P71672_MYCTU | P71672 from UniProtKB/TrEMBL  Length:160

    Alignment length:146
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146      
         P71672_MYCTU     7 PATAEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLVRALTAFTEAGGE 152
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2nyxA01 A:7-151 'winged helix' repressor DNA binding domain                                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyx A   7 PATAEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRmVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQmAPAERHGLVRALTAFTEAGGE 152
                                    16        26        36        46        56        66        76  |     86        96       106       116       126    |  136       146      
                                                                                                   79-MSE                                             131-MSE                 


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with P71672_MYCTU | P71672 from UniProtKB/TrEMBL  Length:160

    Alignment length:147
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       
         P71672_MYCTU    10 AEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLVRALTAFTEAGGEPDAR 156
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2nyxB01 B:10-151 'winged helix' repressor DNA binding domain                                                                                  ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee.........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyx B  10 AEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRmVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQmAPAERHGLVRALTAFTEAGGEPDAR 156
                                    19        29        39        49        59        69        79        89        99       109       119       129 |     139       149       
                                                                                                79-MSE                                             131-MSE                     


Chain C from PDB  Type:PROTEIN  Length:146
 aligned with P71672_MYCTU | P71672 from UniProtKB/TrEMBL  Length:160

    Alignment length:146
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146      
         P71672_MYCTU     7 PATAEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLVRALTAFTEAGGE 152
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2nyxC01 C:7-151 'winged helix' repressor DNA binding domain                                                                                      - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eehhhhhhhhh..hhhhhhhhhhhhhh..eeeee.......eeeeehhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyx C   7 PATAEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRmVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQmAPAERHGLVRALTAFTEAGGE 152
                                    16        26        36        46        56        66        76  |     86        96       106       116       126    |  136       146      
                                                                                                   79-MSE                                             131-MSE                 


Chain D from PDB  Type:PROTEIN  Length:147
 aligned with P71672_MYCTU | P71672 from UniProtKB/TrEMBL  Length:160

    Alignment length:147
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       
         P71672_MYCTU    10 AEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLVRALTAFTEAGGEPDAR 156
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2nyxD01 D:10-151 'winged helix' repressor DNA binding domain                                                                                  ----- CATH domains
           Pfam domains (1) ---------------------------------MarR-2nyxD01 D:43-101                                      ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------MarR-2nyxD02 D:43-101                                      ------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------MarR-2nyxD03 D:43-101                                      ------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------MarR-2nyxD04 D:43-101                                      ------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.eehhhhhhhhh.hhhhhhhhhhhhhhh..eeee.........eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nyx D  10 AEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRmVDRLVGAELIDRLPHPTSRRELLAALTKRGRDVVRQVTEHRRTEIARIVEQmAPAERHGLVRALTAFTEAGGEPDAR 156
                                    19        29        39        49        59        69        79        89        99       109       119       129 |     139       149       
                                                                                                79-MSE                                             131-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  (0, 0)

(no "SCOP Domain" information available for 2NYX)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Family: MarR (16)
(-)
Mycobacterium tuberculosis (1)
1aMarR-2nyxD01D:43-101
1bMarR-2nyxD02D:43-101
1cMarR-2nyxD03D:43-101
1dMarR-2nyxD04D:43-101

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (P71672_MYCTU | P71672)
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.
    GO:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
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.
cellular component
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  Cis Peptide Bonds
    Ala A:10 - Glu A:11   [ RasMol ]  
    Ala A:8 - Thr A:9   [ RasMol ]  
    Ala B:10 - Glu B:11   [ RasMol ]  
    Ala B:155 - Arg B:156   [ RasMol ]  
    Ala C:10 - Glu C:11   [ RasMol ]  
    Ala C:8 - Thr C:9   [ RasMol ]  
    Ala D:10 - Glu D:11   [ RasMol ]  
    Ala D:155 - Arg D:156   [ RasMol ]  
    Arg A:98 - Arg A:99   [ RasMol ]  
    Arg A:99 - Glu A:100   [ RasMol ]  
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    Arg D:98 - Arg D:99   [ RasMol ]  
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    Glu B:12 - Ser B:13   [ RasMol ]  
    Glu D:100 - Leu D:101   [ RasMol ]  
    Glu D:11 - Glu D:12   [ RasMol ]  
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    Gly A:150 - Gly A:151   [ RasMol ]  
    Gly A:151 - Glu A:152   [ RasMol ]  
    Gly C:151 - Glu C:152   [ RasMol ]  
    His D:94 - Pro D:95   [ RasMol ]  
    Pro A:7 - Ala A:8   [ RasMol ]  
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    Pro D:93 - His D:94   [ RasMol ]  
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    Ser D:97 - Arg D:98   [ RasMol ]  
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    Thr D:96 - Ser D:97   [ RasMol ]  
    Val B:14 - Asp B:15   [ RasMol ]  
    Val C:71 - Gln C:72   [ RasMol ]  
 
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