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(-) Description

Title :  CRYSTAL STRUCTURE OF A TRANSCRIPTIONAL REGULATOR (RHA1_RO04179) FROM RHODOCOCCUS SP. RHA1.
 
Authors :  M. Chruszcz, E. Evdokimova, O. Kagan, M. Cymborowski, A. Savchenko, A. A. Joachimiak, W. Minor, Midwest Center For Structural Genomics
Date :  26 Oct 06  (Deposition) - 28 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (1x)
Keywords :  Tetr Family, Transcriptional Regulator, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Chruszcz, E. Evdokimova, O. Kagan, M. Cymborowski, A. Savchenko, A. Edwards, W. Minor, Midwest Center For Structural Genomics (Mcsg)
Crystal Structure Of A Transcriptional Regulator (Rha1_ro04179) From Rhodococcus Sp. Rha1.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidP15TV LIC
    Expression System StrainBL21-CODONPLUS(DE3)-RP
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneRHA1_RO04179
    Organism ScientificRHODOCOCCUS SP.
    Organism Taxid101510
    StrainRHA1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D
Biological Unit 3 (1x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1LMT2Ligand/IonDODECYL-BETA-D-MALTOSIDE
2MSE16Mod. Amino AcidSELENOMETHIONINE
3NDS3Ligand/IonETHYL DIMETHYL AMMONIO PROPANE SULFONATE
Biological Unit 1 (3, 11)
No.NameCountTypeFull Name
1LMT1Ligand/IonDODECYL-BETA-D-MALTOSIDE
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NDS2Ligand/IonETHYL DIMETHYL AMMONIO PROPANE SULFONATE
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1LMT1Ligand/IonDODECYL-BETA-D-MALTOSIDE
2MSE8Mod. Amino AcidSELENOMETHIONINE
3NDS1Ligand/IonETHYL DIMETHYL AMMONIO PROPANE SULFONATE
Biological Unit 3 (3, 21)
No.NameCountTypeFull Name
1LMT2Ligand/IonDODECYL-BETA-D-MALTOSIDE
2MSE16Mod. Amino AcidSELENOMETHIONINE
3NDS3Ligand/IonETHYL DIMETHYL AMMONIO PROPANE SULFONATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:62 , LEU A:69 , VAL A:75 , ARG A:77 , ALA A:84 , ALA A:88 , LYS A:125 , THR A:129 , HOH A:639 , HOH A:718 , GLY B:140 , ASP B:192 , HOH B:639BINDING SITE FOR RESIDUE LMT A 204
2AC2SOFTWAREGLY A:140 , ASP A:192 , HOH A:697 , ARG B:62 , LEU B:69 , SER B:73 , LYS B:125 , THR B:129 , ILE B:130 , HOH B:617 , HOH B:660BINDING SITE FOR RESIDUE LMT B 204
3AC3SOFTWAREGLY A:166 , SER A:167 , PRO A:168 , ALA A:169 , LEU A:170 , HOH A:685 , ALA C:113 , ALA C:114 , PRO D:117BINDING SITE FOR RESIDUE NDS A 601
4AC4SOFTWAREPHE A:59 , ARG A:62 , GLY B:142 , GLY B:190 , ASP B:192BINDING SITE FOR RESIDUE NDS A 602
5AC5SOFTWAREGLY A:142 , GLY A:190 , ASP A:192 , PHE B:59 , ARG B:62BINDING SITE FOR RESIDUE NDS B 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NP5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp C:192 -Val C:193
2Glu D:12 -Arg D:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NP5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NP5)

(-) Exons   (0, 0)

(no "Exon" information available for 2NP5)

(-) 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:187
 aligned with Q0S914_RHOJR | Q0S914 from UniProtKB/TrEMBL  Length:203

    Alignment length:187
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       
         Q0S914_RHOJR     9 TSPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFSTKDEMFAFALRTLVDKLLARLSEVERGGDPARALFAAMSQLLPLDEARSREAHVMAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGMILQGADVVP 195
               SCOP domains d2np5a1 A:9-77 Transcriptional regulator RHA1_ro04179                d2np5a2 A:78-195 Transcriptional regulator RHA1_ro04179                                                                SCOP domains
               CATH domains 2np5A00 A:9-195 Tetracycline Repressor, domain 2                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2np5 A   9 TSPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFSTKDEmFAFALRTLVDKLLARLSEVERGGDPARALFAAmSQLLPLDEARSREAHVmAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGmILQGADVVP 195
                                    18        28        38        48       |58        68        78        88|       98       108       118       128       138       148       158       168       178       188       
                                                                          56-MSE                           89-MSE          106-MSE                                                                         186-MSE     

Chain B from PDB  Type:PROTEIN  Length:187
 aligned with Q0S914_RHOJR | Q0S914 from UniProtKB/TrEMBL  Length:203

    Alignment length:187
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       
         Q0S914_RHOJR     9 TSPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFSTKDEMFAFALRTLVDKLLARLSEVERGGDPARALFAAMSQLLPLDEARSREAHVMAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGMILQGADVVP 195
               SCOP domains d2np5b1 B:9-77 Transcriptional regulator RHA1_ro04179                d2np5b2 B:78-195 Transcriptional regulator RHA1_ro04179                                                                SCOP domains
               CATH domains 2np5B00 B:9-195 Tetracycline Repressor, domain 2                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2np5 B   9 TSPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFSTKDEmFAFALRTLVDKLLARLSEVERGGDPARALFAAmSQLLPLDEARSREAHVmAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGmILQGADVVP 195
                                    18        28        38        48       |58        68        78        88|       98       108       118       128       138       148       158       168       178       188       
                                                                          56-MSE                           89-MSE          106-MSE                                                                         186-MSE     

Chain C from PDB  Type:PROTEIN  Length:184
 aligned with Q0S914_RHOJR | Q0S914 from UniProtKB/TrEMBL  Length:203

    Alignment length:184
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189    
         Q0S914_RHOJR    10 SPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFSTKDEMFAFALRTLVDKLLARLSEVERGGDPARALFAAMSQLLPLDEARSREAHVMAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGMILQGADV 193
               SCOP domains d2np5c1 C:10-77 Transcriptional regulator RHA1_ro04179              d2np5c2 C:78-193 Transcriptional regulator RHA1_ro04179                                                              SCOP domains
               CATH domains 2np5C00 C:10-193 Tetracycline Repressor, domain 2                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2np5 C  10 SPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFSTKDEmFAFALRTLVDKLLARLSEVERGGDPARALFAAmSQLLPLDEARSREAHVmAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGmILQGADV 193
                                    19        29        39        49      | 59        69        79        89        99      |109       119       129       139       149       159       169       179      |189    
                                                                         56-MSE                           89-MSE          106-MSE                                                                         186-MSE   

Chain D from PDB  Type:PROTEIN  Length:158
 aligned with Q0S914_RHOJR | Q0S914 from UniProtKB/TrEMBL  Length:203

    Alignment length:183
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189   
         Q0S914_RHOJR    10 SPERLAAALFDVAAESGLEGASVREVAKRAGVSIGAVQHHFSTKDEMFAFALRTLVDKLLARLSEVERGGDPARALFAAMSQLLPLDEARSREAHVMAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGMILQGAD 192
               SCOP domains d2np5d1 D:10-77 Tr                         anscriptional regulator Rd2np5d2 D:78-192 Transcriptional regulator RHA1_ro04179                                                             SCOP domains
               CATH domains 2np5D00 D:10-192 T                         etracycline Repressor, domain 2                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.-------------------------hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2np5 D  10 SPERLAAALFDVAAESGL-------------------------KDEmFAFALRTLVDKLLARLSEVERGGDPARALFAAmSQLLPLDEARSREAHVmAAFAVRAATSPSLAEIRRKTLFTIRTGLSAVLIGIGTPEAETRAALLLATVDGLALDAIGSPALYPPEYLEHALDIQIGmILQGAD 192
                                    19       | -         -         -   |  | 59        69        79        89        99      |109       119       129       139       149       159       169       179      |189   
                                            27                        53  |                               89-MSE          106-MSE                                                                         186-MSE  
                                                                         56-MSE                                                                                                                                    

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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  (2, 8)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2NP5)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q0S914_RHOJR | Q0S914)
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: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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