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(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF STREPTOCOCCUS DYSGALACTIAE SHP PHEROMONE RECEPTOR RGG2
 
Authors :  M. B. Neiditch, V. Parashar
Date :  19 Mar 15  (Deposition) - 08 Apr 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Dna Binding, Pheromone Binding, Repeat Domain, Quorum Sensing, Dna Binding Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Parashar, C. Aggarwal, M. J. Federle, M. B. Neiditch
Rgg Protein Structure-Function And Inhibition By Cyclic Peptide Compounds.
Proc. Natl. Acad. Sci. Usa V. 112 5177 2015
PubMed-ID: 25847993  |  Reference-DOI: 10.1073/PNAS.1500357112

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MUTR
    Organism Scientific: STREPTOCOCCUS DYSGALACTIAE
    Organism Taxid: 1334
    Strain: LT1
 
Molecule 2 - CYCLOSPORIN A
    Chains: E, F, G, H
    Engineered: YES
    Organism Scientific: HYPOCREA PACHYBASIOIDES
    Organism Taxid: 40695
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 61)

Asymmetric Unit (8, 61)
No.NameCountTypeFull Name
1ABA4Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2BMT4Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
3DAL4Mod. Amino AcidD-ALANINE
4MLE16Mod. Amino AcidN-METHYLLEUCINE
5MSE12Mod. Amino AcidSELENOMETHIONINE
6MVA4Mod. Amino AcidN-METHYLVALINE
7SAR4Mod. Amino AcidSARCOSINE
8SO413Ligand/IonSULFATE ION
Biological Unit 1 (8, 30)
No.NameCountTypeFull Name
1ABA2Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2BMT2Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
3DAL2Mod. Amino AcidD-ALANINE
4MLE8Mod. Amino AcidN-METHYLLEUCINE
5MSE6Mod. Amino AcidSELENOMETHIONINE
6MVA2Mod. Amino AcidN-METHYLVALINE
7SAR2Mod. Amino AcidSARCOSINE
8SO46Ligand/IonSULFATE ION
Biological Unit 2 (8, 31)
No.NameCountTypeFull Name
1ABA2Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2BMT2Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
3DAL2Mod. Amino AcidD-ALANINE
4MLE8Mod. Amino AcidN-METHYLLEUCINE
5MSE6Mod. Amino AcidSELENOMETHIONINE
6MVA2Mod. Amino AcidN-METHYLVALINE
7SAR2Mod. Amino AcidSARCOSINE
8SO47Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:255 , TYR A:263 , GLN B:32 , SER B:41binding site for residue SO4 A 301
02AC2SOFTWAREASN A:156 , TYR A:157 , TYR A:198 , HOH A:408 , HOH A:431 , HOH A:473 , SO4 D:304binding site for residue SO4 A 302
03AC3SOFTWARESER A:44 , CYS A:45 , SER A:46 , LEU B:5 , PHE B:36 , ILE B:43binding site for residue SO4 A 303
04AC4SOFTWAREHIS A:101binding site for residue SO4 A 304
05AC5SOFTWAREARG B:13 , GLN B:14 , HOH B:408binding site for residue SO4 B 301
06AC6SOFTWAREHIS B:27 , SER B:46 , ARG B:47 , ASN B:50binding site for residue SO4 B 302
07AC7SOFTWARETHR B:169 , TYR B:206 , LYS B:210 , HIS C:231 , LYS C:235 , HOH C:402 , HOH C:435binding site for residue SO4 C 301
08AC8SOFTWAREHIS C:101 , HOH C:429 , HOH C:499binding site for residue SO4 C 302
09AC9SOFTWAREARG C:79 , ASP C:98 , TYR C:99 , HOH C:429binding site for residue SO4 C 303
10AD1SOFTWAREARG D:13 , GLN D:14 , HOH D:403binding site for residue SO4 D 301
11AD2SOFTWARETYR C:263 , LYS C:267 , SER D:31 , SER D:34 , ARG D:38binding site for residue SO4 D 302
12AD3SOFTWAREGLN D:32 , ARG D:35binding site for residue SO4 D 303
13AD4SOFTWARESO4 A:302 , HOH A:408 , HOH A:410 , PHE D:161 , LYS D:165 , TYR D:206binding site for residue SO4 D 304
14AD5SOFTWAREARG A:81 , LYS A:87 , TYR A:142 , GLY A:149 , ASN A:150 , ARG A:153 , ASN A:190 , LYS B:178 , ASP B:217 , HOH E:101 , HOH E:102 , HOH E:103BINDING SITE FOR CHAIN E OF CYCLOSPORIN A
15AD6SOFTWAREARG B:81 , ILE B:112 , ILE B:146 , ASN B:150 , LEU B:183 , GLN B:186 , ASN B:190 , ILE B:193 , TYR B:222 , LEU B:262BINDING SITE FOR CHAIN F OF CYCLOSPORIN A
16AD7SOFTWAREARG C:81 , ILE C:112 , ILE C:146 , ASN C:150 , LEU C:183 , GLN C:186 , ASN C:190 , ILE C:193 , TYR C:222 , LEU C:262 , ASP D:217 , HOH G:101 , HOH G:102 , HOH G:103BINDING SITE FOR CHAIN G OF CYCLOSPORIN A
17AD8SOFTWAREARG D:81 , ILE D:112 , ILE D:146 , ASN D:150 , ARG D:153 , GLN D:186 , ASN D:190 , TYR D:222 , LEU D:262 , HOH D:410 , HOH H:101 , HOH H:102 , HOH H:103BINDING SITE FOR CHAIN H OF CYCLOSPORIN A

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:45 -B:45
2C:45 -D:45

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Mva E:4 -Bmt E:5
2Mva F:4 -Bmt F:5
3Aba F:6 -Sar F:7
4Val F:9 -Mle F:10
5Mva G:4 -Bmt G:5
6Aba G:6 -Sar G:7
7Val G:9 -Mle G:10
8Mva H:4 -Bmt H:5
9Aba H:6 -Sar H:7
10Val H:9 -Mle H:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YV9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YV9)

(-) Exons   (0, 0)

(no "Exon" information available for 4YV9)

(-) 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:261
                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh.........hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yv9 A   5 LGKTLRRLRQGKQVSISSLLSKSQISRFERGESEISCSRLLNLLDKLNITIDEFVSTTHFFTLLSRVRKYYAEKNVAKLLKLLEDYAHKDYESTmIKAILSSIEPTVEPSEEEVTRLTDYLFSVEQWGYYEIILLGNCSRFINYNTLFLLTKEmVTSFAYSEQNKTNKTLVTQLSINCLIISIDYSYFDHSHYLIEKIEFLLRDELNFYEKTVFLYVHGYYKLKQGQVSGKDDmRQALQIFKYLGEDALYYSYKEHYRKEV 274
                                    14        28        38        48        58      ||73        83        93       103    |  113       123       133       143       153       163   |   173       183       193       203       213       223       233       243   |   253       263       273 
                                             23|                                   65|                                  108-MSE                                                    167-MSE                                                                         247-MSE                       
                                              28                                    71                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhh........hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yv9 B   5 LGKTLRRLRQGKQVSISSLADEHLSKSQISRFERGESEISCSRLLNLLDKLNITIDEFVSTHSKTHTHFFTLLSRVRKYYAEKNVAKLLKLLEDYAHKDYESTmIKAILSSIEPTVEPSEEEVTRLTDYLFSVEQWGYYEIILLGNCSRFINYNTLFLLTKEmVTSFAYSEQNKTNKTLVTQLSINCLIISIDYSYFDHSHYLIEKIEFLLRDELNFYEKTVFLYVHGYYKLKQGQVSGKDDmRQALQIFKYLGEDALYYSYKEHYRKEV 274
                                    14        24        34        44        54        64        74        84        94       104   |   114       124       134       144       154       164  |    174       184       194       204       214       224       234       244  |    254       264       274
                                                                                                                                 108-MSE                                                    167-MSE                                                                         247-MSE                       


Chain C from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yv9 C   4 ELGKTLRRLRQGKQVSISSLADEHLSKSQISRFERGESEISCSRLLNLLDKLNITIDEFVSTHHTHFFTLLSRVRKYYAEKNVAKLLKLLEDYAHKDYESTmIKAILSSIEPTVEPSEEEVTRLTDYLFSVEQWGYYEIILLGNCSRFINYNTLFLLTKEmVTSFAYSEQNKTNKTLVTQLSINCLIISIDYSYFDHSHYLIEKIEFLLRDELNFYEKTVFLYVHGYYKLKQGQVSGKDDmRQALQIFKYLGEDALYYSYKEHYRKEV 274
                                    13        23        33        43        53        63  ||    76        86        96       106 |     116       126       136       146       156       166|      176       186       196       206       216       226       236       246|      256       266        
                                                                                         66|                                   108-MSE                                                    167-MSE                                                                         247-MSE                       
                                                                                          70                                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh..hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yv9 D   4 ELGKTLRRLRQGKQVSISSLADEHLSKSQISRFERGESEISCSRLLNLLDKLNITIDEFVSTHSTHFFTLLSRVRKYYAEKNVAKLLKLLEDYAHKDYESTmIKAILSSIEPTVEPSEEEVTRLTDYLFSVEQWGYYEIILLGNCSRFINYNTLFLLTKEmVTSFAYSEQNKTNKTLVTQLSINCLIISIDYSYFDHSHYLIEKIEFLLRDELNFYEKTVFLYVHGYYKLKQSGKDDmRQALQIFKYLGEDALYYSYKEHYRKE 273
                                    13        23        33        43        53        63   ||   76        86        96       106 |     116       126       136       146       156       166|      176       186       196       206       216       226       236 ||    249       259       269    
                                                                                          67|                                  108-MSE                                                    167-MSE                                                                238|    |                          
                                                                                           71                                                                                                                                                                     242    |                          
                                                                                                                                                                                                                                                                       247-MSE                      


Chain E from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4yv9 E   1 xxxxxxxxVxA  11
                            ||||||||10 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE
                                    10-MLE


Chain F from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4yv9 F   1 xxxxxxxxVxA  11
                            ||||||||10 
                            |||||||| | 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE


Chain G from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4yv9 G   1 xxxxxxxxVxA  11
                            ||||||||10 
                            |||||||| | 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE


Chain H from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 4yv9 H   1 xxxxxxxxVxA  11
                            ||||||||10 
                            |||||||| | 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE
   Legend:   → Mismatch (orange background)
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  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 4YV9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YV9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YV9)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YV9)

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  4yv9
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  A0A0J9X288_S | A0A0J9X288
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A0A0J9X288_S | A0A0J9X288: 4yv6

(-) Related Entries Specified in the PDB File

4yv6 4YV6 CONTAINS THE SAME RGG PROTEIN WITHOUT BOUND CYCLOSPORIN A