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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FULL-LENGTH SORBITOL OPERON REGULATOR SORC FROM KLEBSIELLA PNEUMONIAE
 
Authors :  D. De Sanctis, C. E. Mcvey, F. J. Enguita, M. A. Carrondo
Date :  21 Nov 08  (Deposition) - 05 May 09  (Release) - 05 May 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sorc, Activator, Repressor, Dna-Binding, Transcription, Klebsiella Pneumoniae, Transcription Regulator, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. De Sanctis, C. E. Mcvey, F. J. Enguita, M. A. Carrondo
Crystal Structure Of The Full-Length Sorbitol Operon Regulator Sorc From Klebsiella Pneumoniae: Structural Evidence For A Novel Transcriptional Regulation Mechanism.
J. Mol. Biol. V. 387 759 2009
PubMed-ID: 19232357  |  Reference-DOI: 10.1016/J.JMB.2009.02.017

(-) Compounds

Molecule 1 - SORBITOL OPERON REGULATOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
    Synonym: SORC TRANSCRIPTION REGULATOR, SOR OPERON ACTIVATOR

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
4MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP D:117 , GLY D:118 , ARG D:119 , ALA D:120 , VAL D:121 , GLY D:211BINDING SITE FOR RESIDUE GOL D1316
2AC2SOFTWARESER A:116 , TRP A:117 , GLY A:211 , ASP A:243 , ILE A:244 , CYS A:245BINDING SITE FOR RESIDUE GOL A1316
3AC3SOFTWARETRP A:117 , PRO A:146 , ALA A:178 , LEU A:179 , PHE A:226 , TYR A:227BINDING SITE FOR RESIDUE MPD A1317
4AC4SOFTWARESER B:204 , LEU B:205 , ASP B:206 , GLN B:274 , ALA B:275 , ARG B:276BINDING SITE FOR RESIDUE MRD B1316
5AC5SOFTWAREGLU A:126BINDING SITE FOR RESIDUE CL A1318

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W48)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:4 -Asp B:5

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W48)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W48)

(-) Exons   (0, 0)

(no "Exon" information available for 2W48)

(-) 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:308
 aligned with SORC_KLEPN | P37078 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  
           SORC_KLEPN     4 SDDIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFGLKEAVVASSDGLLEEEQLSAMGQHGALLVDRLLEPGDIIGFSWGRAVRSLVENLPQRSQSRQVICVPIIGGPSGKLESRYHVNTLTYGAAARLKAESHLADFPALLDNPLIRNGIMQSQHFKTISSYWDSLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGGLVDTNMSEKTLSIEMAKLRQARYSIGIAMGEEKYSGILGALHGRYINCLVTNRETAELLLK 315
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh..eeeee..----.hhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhh...........eeee.........hhhhhhhhhhhhhhhhh..ee..........hhhhhhhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhhh.eeeee..eeee.........hhhh....hhhhhhh..eeeee..hhhhhhhhhhhhhh....eeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w48 A   4 SDDIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFGLKEAVVASS----EEEQLSAMGQHGALLVDRLLEPGDIIGFSWGRAVRSLVENLPQRSQSRQVICVPIIGGPSGKLESRYHVNTLTYGAAARLKAESHLADFPALLDNPLIRNGIMQSQHFKTISSYWDSLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGGLVDTNMSEKTLSIEMAKLRQARYSIGIAMGEEKYSGILGALHGRYINCLVTNRETAELLLK 315
                                    13        23        33        43        53        63        73        83    |   93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  
                                                                                                          83   88                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:313
 aligned with SORC_KLEPN | P37078 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:313
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312   
           SORC_KLEPN     3 NSDDIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFGLKEAVVASSDGLLEEEQLSAMGQHGALLVDRLLEPGDIIGFSWGRAVRSLVENLPQRSQSRQVICVPIIGGPSGKLESRYHVNTLTYGAAARLKAESHLADFPALLDNPLIRNGIMQSQHFKTISSYWDSLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGGLVDTNMSEKTLSIEMAKLRQARYSIGIAMGEEKYSGILGALHGRYINCLVTNRETAELLLK 315
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh..........eeee.........hhhhhhhhhhhhhhhhhh.ee..........hhhhhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhhhhhhhhhhh...eee..eee.....ee.hhhhhh....hhhhhhh..eeeee.....hhhhhhhhhhh....eeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w48 B   3 NSDDIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFGLKEAVVASSDGLLEEEQLSAMGQHGALLVDRLLEPGDIIGFSWGRAVRSLVENLPQRSQSRQVICVPIIGGPSGKLESRYHVNTLTYGAAARLKAESHLADFPALLDNPLIRNGIMQSQHFKTISSYWDSLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGGLVDTNMSEKTLSIEMAKLRQARYSIGIAMGEEKYSGILGALHGRYINCLVTNRETAELLLK 315
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312   


Chain C from PDB  Type:PROTEIN  Length:299
 aligned with SORC_KLEPN | P37078 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:312
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313  
           SORC_KLEPN     4 SDDIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFGLKEAVVASSDGLLEEEQLSAMGQHGALLVDRLLEPGDIIGFSWGRAVRSLVENLPQRSQSRQVICVPIIGGPSGKLESRYHVNTLTYGAAARLKAESHLADFPALLDNPLIRNGIMQSQHFKTISSYWDSLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGGLVDTNMSEKTLSIEMAKLRQARYSIGIAMGEEKYSGILGALHGRYINCLVTNRETAELLLK 315
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhh...hhhhhhhhh.....hhhhhhhhhh......eee....hhhhhhhhhhhhhhh..eeeee--------.hhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhh...........eeee.........hhhhhhhhhhhhhhhhh..ee..........hhhhhhhhhhhhhhhhhhhhhh...eeeee.....--...hhhhhhhhhhhhhhhhh.eeeee..eeee....---hhhhhh....hhhhhhh..eeeee..hhhhhhhhhhhhhh....eeeeehhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w48 C   4 SDDIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFGLKEAVVA--------EQLSAMGQHGALLVDRLLEPGDIIGFSWGRAVRSLVENLPQRSQSRQVICVPIIGGPSGKLESRYHVNTLTYGAAARLKAESHLADFPALLDNPLIRNGIMQSQHFKTISSYWDSLDVALVGIGSPA--DGANWHAFYGSEESDDLNARHVAGDICSRFYDINGG---TNMSEKTLSIEMAKLRQARYSIGIAMGEEKYSGILGALHGRYINCLVTNRETAELLLK 315
                                    13        23        33        43        53        63        73       | -      | 93       103       113       123       133       143       153       163       173       183       193       203       213  |  | 223       233       243       253|   |  263       273       283       293       303       313  
                                                                                                        81       90                                                                                                                           216  |                                254 258                                                         
                                                                                                                                                                                                                                                 219                                                                                                


Chain D from PDB  Type:PROTEIN  Length:308
 aligned with SORC_KLEPN | P37078 from UniProtKB/Swiss-Prot  Length:315

    Alignment length:313
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312   
           SORC_KLEPN     3 NSDDIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFGLKEAVVASSDGLLEEEQLSAMGQHGALLVDRLLEPGDIIGFSWGRAVRSLVENLPQRSQSRQVICVPIIGGPSGKLESRYHVNTLTYGAAARLKAESHLADFPALLDNPLIRNGIMQSQHFKTISSYWDSLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGGLVDTNMSEKTLSIEMAKLRQARYSIGIAMGEEKYSGILGALHGRYINCLVTNRETAELLLK 315
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----HTH_38-2w48D01 D:8-45                 -----------Sugar-bind-2w48D05 D:57-315                                                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) -----HTH_38-2w48D02 D:8-45                 -----------Sugar-bind-2w48D06 D:57-315                                                                                                                                                                                                                                         Pfam domains (2)
           Pfam domains (3) -----HTH_38-2w48D03 D:8-45                 -----------Sugar-bind-2w48D07 D:57-315                                                                                                                                                                                                                                         Pfam domains (3)
           Pfam domains (4) -----HTH_38-2w48D04 D:8-45                 -----------Sugar-bind-2w48D08 D:57-315                                                                                                                                                                                                                                         Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhh..........eeee.........hhhhhhhhhhhhhhhhhh.ee..........hhhhhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhh.hhhhhhhhhh...eee..eee......-----.......hhhhhhh..eeeee.....hhhhhhhhhhh....eeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w48 D   3 NSDDIRLIVKIAQLYYEQDMTQAQIARELGIYRTTISRLLKRGREQGIVTIAINYDYNENLWLEQQLKQKFGLKEAVVASSDGLLEEEQLSAMGQHGALLVDRLLEPGDIIGFSWGRAVRSLVENLPQRSQSRQVICVPIIGGPSGKLESRYHVNTLTYGAAARLKAESHLADFPALLDNPLIRNGIMQSQHFKTISSYWDSLDVALVGIGSPAIRDGANWHAFYGSEESDDLNARHVAGDICSRFYDINGGL-----SEKTLSIEMAKLRQARYSIGIAMGEEKYSGILGALHGRYINCLVTNRETAELLLK 315
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  |    262       272       282       292       302       312   
                                                                                                                                                                                                                                                                                      255   261
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 2W48)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W48)

(-) Pfam Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: ISOCOT_Fold (53)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SORC_KLEPN | P37078)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
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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  2w48
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 Related Entries

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