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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS SUBTILIS GABR AT 2.05 ANGSTROMS RESOLUTION
 
Authors :  M. Goto, K. Okuda, T. Yoshimura
Date :  26 Jun 14  (Deposition) - 24 Dec 14  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Transcriptional Regulator, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Okuda, S. Kato, T. Ito, S. Shiraki, Y. Kawase, M. Goto, S. Kawashima, H. Hemmi, H. Fukada, T. Yoshimura
Role Of The Aminotransferase Domain In Bacillus Subtilis Gabr, A Pyridoxal 5'-Phosphate-Dependent Transcriptional Regulator
Mol. Microbiol. V. 95 245 2015
PubMed-ID: 25388514  |  Reference-DOI: 10.1111/MMI.12861

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATORY PROTEIN GABR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD18
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GABR, YCNF, BSU03890
    Organism Scientific: BACILLUS SUBTILIS 168
    Organism Taxid: 224308
    Other Details: LYS312 MAKES A SCHIFF BASE WITH PLP.

 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, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1LLP4Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1LLP2Mod. Amino Acid(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 4TV7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4TV7)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Glu A:202 -Pro A:203
2Phe A:250 -Pro A:251
3Glu B:202 -Pro B:203
4Phe B:250 -Pro B:251
5Glu C:202 -Pro C:203
6Phe C:250 -Pro C:251
7Glu D:202 -Pro D:203
8Phe D:250 -Pro D:251

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4TV7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4TV7)

(-) Exons   (0, 0)

(no "Exon" information available for 4TV7)

(-) 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:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh.......ee.hhhhhhhhh..hhhhhhhhhhhhhhh..eeee...eeee..........hhhhh.....ee.........hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhh...eeeeeee..eehhhhhhhh...eeee............hhhhhhhhhhhhhh....eeeeee.............hhhhhh....eeeeee...........eeee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............eeee.....hhhhhhhhhhhh.ee.ee.hhh...eeee....hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4tv7 A   4 TITLDRSEQADYIYQQIYQKLKKEILSRNLLPHSKVPSKRELAENLKVSVNSVNSAYQQLLAEGYLYAIERKGFFVEELDMFSAALPDDLKEIHIWISFSHMDTDHFPIKSWFRCEQKAASRSYMSHPQGIYEVRAAITRLISLTRGVKCRPEQMIIGAGTQVLMQLLTELLPKEAVYAMEEPGYRRMYQLLKNAGKQVKTIMLDEKGMSIAEITRQQPDVLVTTPSHQFPSGTIMPVSRRIQLLNWAAEEPRRYIIEDDYDSEFTYDVDSIPALQSLDRFQNVIYMGTFSkSLLPGLRISYMVLPPELLRAYKQRGYDLQTCSSLTQLTLQEFIESGEYQKHIKKMKQHYKEKRERLITALEAEFSGEVTVKGANAGLHFVTEDTRRTEQDILSHAAGLQLEIFGMSRFRPALIIGFARLKEEDIQEGVQR 463
                                    13        23        33        43        53        63        73        83   ||   99    || 113 ||    125       135   ||  150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310 |     320       330       340       350       360       370       380       390       400   ||  411       421       431|      451       461  
                                                                                                              87|       104|   115|                  139|                                                                                                                                                                    312-LLP                                                                                     404|                      431|                     
                                                                                                               94        109    118                   145                                                                                                                                                                                                                                                                 406                       442                     


Chain B from PDB  Type:PROTEIN  Length:430
                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhh.........hhhhhhh..hhhhhhhhhhhhhhh..ee....ee........hhhhh.....ee...........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhh...eeeeeee..eehhhhhhhh...eeee............hhhhhhhhhhhhhh....eeeee..............hhhhhh....eeeeee...........eeee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee......eeeeee....hhhhhhhhhhh..ee.ee.hhhh...eeeee....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tv7 B   9 RSEQADYIYQQIYQKLKKEILSRNLLPHSVPSKRELAEKVSVNSVNSAYQQLLAEGYLYAKGFFVEELDMFSLPDDLKEISDWISFSHMSSDTDHFPIKSWFRCEQKAASRHPQGIYEVRAAITRLISLTRGVKCRPEQMIIGAGTQVLMQLLTELLPKEAVYAMEEPGYRRMYQLLKNAGKQVKTIMLDEKGMSIAEITRQQPDVLVTTPSHQFPSGTIMPVSRRIQLLNWAAEEPRRYIIEDDYDSEFTYDVDSIPALQSLDRFQNVIYMGTFSkSLLPGLRISYMVLPPELLRAYKQRGYDLQTCSSLTQLTLQEFIESGEYQKHIKKMKQHYKEKRERLITALEAEFSGEVTVKGANAGLHFVTEFDTRRTEQDILSHAAGLQLEIFGMSRFNLRPALIIGFARLKEEDIQEGVQRLFKAVYGHKK 473
                                    18        28        39       |51        61        71|       84 ||    102|      116       126       136||     155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      |315       325       335       345       355       365       375       385       395       405       415       425       443       453       463       473
                                                       37|      47|                   71|         86|    102|                           137|                                                                                                                                                                  312-LLP                                                                                                                  433|                               
                                                        39       50                    75          95     107                            147                                                                                                                                                                                                                                                                                            442                               


Chain C from PDB  Type:PROTEIN  Length:452
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee.........hhhhh........ee...........hhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhh...eeeeeee..eehhhhhhhh...eeee............hhhhhhhhhhhhhh....eeeee..............hhhhhh....eeeeee...........eeee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee......eeeeee....hhhhhhhhhhh..ee.ee.hhhh...eeeee....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tv7 C   4 TITLDRSEQADYIYQQIYQKLKKEILSRNLLPHSKVPSKRELAENLKVSVNSVNSAYQQLLAEGYLYAIERKGFFVEELDMFSALPDDLKEIHDQSDWISFSHMSSDTDHFPIKSWFRCEQKAASRSYRTLMSHPQGIYEVRAAITRLISLTRGVKCRPEQMIIGAGTQVLMQLLTELLPKEAVYAMEEPGYRRMYQLLKNAGKQVKTIMLDEKGMSIAEITRQQPDVLVTTPSHQFPSGTIMPVSRRIQLLNWAAEEPRRYIIEDDYDSEFTYDVDSIPALQSLDRFQNVIYMGTFSkSLLPGLRISYMVLPPELLRAYKQRGYDLQTCSSLTQLTLQEFIESGEYQKHIKKMKQHYKEKRERLITALEAEFSGEVTVKGANAGLHFVTEFDTRRTEQDILSHAAGLQLEIFGMSRFNLRPALIIGFARLKEEDIQEGVQRLFKAVYGHKK 473
                                    13        23        33        43        53        63        73        83  ||   100  ||   111       121       131       141||     153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433|      451       461       471  
                                                                                                             86|      103|                                  142|                                                                                                                                                                    312-LLP                                                                                                                  433|                               
                                                                                                              94       105                                   145                                                                                                                                                                                                                                                                                              442                               


Chain D from PDB  Type:PROTEIN  Length:449
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhhh.eeee...eeee............hhhhh......ee...........hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...hhh.eeee.hhhhhhhhhhhhh.....eeeee..hhhhhhhhhhh...eeeeeee..eehhhhhhhh...eeee............hhhhhhhhhhhhhhh...eeeee...............hhhhh....eeeeee...........eeee.hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee......eeeeee....hhhhhhhhhhhh.ee.ee.hhhh....eeeee....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tv7 D   5 ITLDRSEQADYIYQQIYQKLKKEILSRNLLPHSKVPSKRELAENLKVSVNSVNSAYQQLLAEGYLYAIERKGFFVEELDMFSAEFALPDDLKEIHSDWISFSHMSSDTDHFPIKSWFRCEQKAASRSYRTSHPQGIYEVRAAITRLISLTRGVKCRPEQMIIGAGTQVLMQLLTELLPKEAVYAMEEPGYRRMYQLLKNAGKQVKTIMLDEKGMSIAEITRQQPDVLVTTPSHQFPSGTIMPVSRRIQLLNWAAEEPRRYIIEDDYDSEFTYDVDSIPALQSLDRFQNVIYMGTFSkSLLPGLRISYMVLPPELLRAYKQRGYDLQTCSSLTQLTLQEFIESGEYQKHIKKMKQHYKEKRERLITALEAEFSGEVTVKGANAGLHFVTEFDTRRTEQDILSHAAGLQLEIFGMSRFNLKRPALIIGFARLKEEDIQEGVQRLFKAVYGH 471
                                    14        24        34        44        54        64        74        84   ||   98    || 111       121       131       141|      155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305      |315       325       335       345       355       365       375       385       395       405       415       425       442       452       462         
                                                                                                              88|       103|                               141|                                                                                                                                                                   312-LLP                                                                                                                   434|                             
                                                                                                               93        107                                146                                                                                                                                                                                                                                                                                              442
   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 4TV7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4TV7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4TV7)

(-) Gene Ontology  (9, 9)

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  Cis Peptide Bonds
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    Glu B:202 - Pro B:203   [ RasMol ]  
    Glu C:202 - Pro C:203   [ RasMol ]  
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  4tv7
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 Related Entries

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

UniProtKB/Swiss-Prot
        GABR_BACSU | P94426: 4mgr 4n0b 5t4j 5t4k 5x03

(-) Related Entries Specified in the PDB File

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