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(-) Description

Title :  CRYSTAL STRUCTURE OF YVOA FROM BACILLUS SUBTILIS IN COMPLEX WITH GLUCOSAMINE-6-PHOSPHATE
 
Authors :  S. B. Fillenberg, Y. A. Muller
Date :  14 Jul 14  (Deposition) - 14 Jan 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transcription, Repressor, Bacterial Transcription Regulation, Transcription Factor, Gntr/Hutc Family, Chorismate Lyase Fold, N- Acetylglucosamine Utilization (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. B. Fillenberg, F. C. Grau, G. Seidel, Y. A. Muller
Structural Insight Into Operator Dre-Sites Recognition And Effector Binding In The Gntr/Hutc Transcription Regulator Nagr.
Nucleic Acids Res. V. 43 1283 2015
PubMed-ID: 25564531  |  Reference-DOI: 10.1093/NAR/GKU1374

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REPRESSOR YVOA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: YVOA, BSU35030
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid: 224308

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric/Biological Unit (2, 26)
No.NameCountTypeFull Name
1EDO24Ligand/Ion1,2-ETHANEDIOL
2GLP2Ligand/IonGLUCOSAMINE 6-PHOSPHATE

(-) Sites  (26, 26)

Asymmetric Unit (26, 26)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:88 , PHE A:89 , THR A:90 , ARG A:133 , ARG A:135 , GLU A:145 , SER A:164 , SER A:165 , ILE A:166 , TYR A:167 , ARG A:211 , GLU A:222 , ALA A:224 , TYR A:228 , EDO A:302 , HOH A:453 , HOH A:454binding site for residue GLP A 301
02AC2SOFTWAREGLN A:183 , ILE A:209 , ARG A:211 , TYR A:228 , GLP A:301 , HOH A:461 , HOH A:518 , HOH A:547binding site for residue EDO A 302
03AC3SOFTWAREGLN A:84 , TYR A:238 , ASP A:240 , GLN B:84binding site for residue EDO A 303
04AC4SOFTWARETYR A:13 , MET A:16 , GLU A:17 , LYS A:20binding site for residue EDO A 304
05AC5SOFTWAREASN A:158 , SER A:179 , GLN A:216 , HOH A:478binding site for residue EDO A 305
06AC6SOFTWARETYR A:173 , HOH A:408 , HOH A:511 , HOH A:542binding site for residue EDO A 306
07AC7SOFTWARELEU A:157binding site for residue EDO A 307
08AC8SOFTWARELYS A:130 , HIS A:148binding site for residue EDO A 308
09AC9SOFTWAREGLU A:184 , GLU A:186 , LEU A:208 , LYS A:210binding site for residue EDO A 309
10AD1SOFTWAREPRO A:10 , ILE A:11 , TYR A:12 , THR A:50 , HOH A:409 , LYS B:130binding site for residue EDO A 310
11AD2SOFTWAREGLU A:186 , SER A:188 , EDO A:313 , HOH A:501 , GLN B:6binding site for residue EDO A 311
12AD3SOFTWAREGLU A:17 , LYS A:20 , LYS A:24 , ASN B:196binding site for residue EDO A 312
13AD4SOFTWARESER A:188 , ALA A:189 , GLU A:194 , VAL A:227 , EDO A:311 , ASN B:4 , SER B:7binding site for residue EDO A 313
14AD5SOFTWAREGLU A:91 , TYR A:167 , ASP A:168 , GLU A:171 , ARG B:241binding site for residue EDO A 314
15AD6SOFTWARESER B:88 , PHE B:89 , THR B:90 , ARG B:133 , ARG B:135 , GLU B:145 , SER B:164 , SER B:165 , ILE B:166 , TYR B:167 , ARG B:211 , GLU B:222 , TYR B:228 , HOH B:440 , HOH B:441binding site for residue GLP B 301
16AD7SOFTWAREMET B:16 , GLU B:17 , LYS B:20 , GLU B:61binding site for residue EDO B 302
17AD8SOFTWAREGLU B:156 , ASN B:158 , ASN B:217binding site for residue EDO B 303
18AD9SOFTWAREGLU B:152 , ASN B:174 , EDO B:305 , HOH B:476binding site for residue EDO B 304
19AE1SOFTWARELEU B:153 , ASN B:174 , LEU B:215 , ASN B:217 , THR B:219 , EDO B:304 , HOH B:428binding site for residue EDO B 305
20AE2SOFTWARESER A:7 , SER B:188 , ALA B:189 , GLU B:194 , VAL B:227binding site for residue EDO B 306
21AE3SOFTWARELYS B:182 , THR B:212 , TYR B:214binding site for residue EDO B 307
22AE4SOFTWARELYS A:130 , PRO B:10 , ILE B:11 , TYR B:12 , THR B:50binding site for residue EDO B 308
23AE5SOFTWARETHR A:234 , GLU B:184 , GLU B:186 , LEU B:208 , LYS B:210binding site for residue EDO B 309
24AE6SOFTWAREARG A:241 , GLU B:91 , TYR B:167 , ASP B:168 , GLU B:171 , HOH B:444binding site for residue EDO B 310
25AE7SOFTWARELEU A:86 , ARG B:241binding site for residue EDO B 311
26AE8SOFTWAREMET A:239 , GLN B:81 , LEU B:83 , GLN B:183 , ILE B:209 , ARG B:211 , TYR B:228 , HOH B:448binding site for residue EDO B 312

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U0V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1His A:124 -Pro A:125
2His B:124 -Pro B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U0V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U0V)

(-) Exons   (0, 0)

(no "Exon" information available for 4U0V)

(-) Sequences/Alignments

Asymmetric/Biological 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:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee....eeee.....hhhhhhhhh...eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee..eeeeeeeeeee.hhh...hhhhhh.hhhhhhhhhhh..eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee....eeeeeeeeee...eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0v A   0 HMNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVSKPKMEQALQGLTSFTEDMKSRGMTPGSRLIDYQLIDSTEELAAILGCGHPSSIHKITRVRLANDIPMAIESSHIPFELAGELNESHFQSSIYDHIERYNSIPISRAKQELEPSAATTEEANILGIQKGAPVLLIKRTTYLQNGTAFEHAKSVYRGDRYTFVHYMDRL 242
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239   


Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh..........hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee...eeee....eeee.....hhhhhhhh....eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee..eeeeeeeeeee.hhh...hhhhhh.hhhhhhhhhhh..eeeeeeeeeeee.hhhhhhhhh.....eeeeeeeeeee....eeeeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0v B   0 HMNINKQSPIPIYYQIMEQLKTQIKNGELQPDMPLPSEREYAEQFGISRMTVRQALSNLVNEGLLYRLKGRGTFVSKPKMEQALQGLTSFTEDMKSRGMTPGSRLIDYQLIDSTEELAAILGCGHPSSIHKITRVRLANDIPMAIESSHIPFELAGELNESHFQSSIYDHIERYNSIPISRAKQELEPSAATTEEANILGIQKGAPVLLIKRTTYLQNGTAFEHAKSVYRGDRYTFVHYMDR 241
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239
   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 4U0V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U0V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U0V)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4u0v
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  YVOA_BACSU | O34817
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 Related Entries

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

UniProtKB/Swiss-Prot
        YVOA_BACSU | O34817: 2wv0 4u0w 4u0y 4wwc

(-) Related Entries Specified in the PDB File

2wv0 2WV0 CONTAINS THE SAME PROTEIN COMPLEXED WITH A SULFATE ION