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(-) Description

Title :  CRYSTAL STRUCTURE OF A TWO-COMPONENT RESPONSE REGULATOR FROM CLOSTRIDIUM DIFFICILE
 
Authors :  R. Sugadev, S. K. Burley, S. Swaminathan, New York Sgx Research Cen Structural Genomics (Nysgxrc)
Date :  16 Aug 07  (Deposition) - 04 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.89
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Keywords :  11017X, Psi-Ii, Structural Genomics, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Dna- Binding, Phosphorylation, Transcription, Transcription Regulation, Two-Component Regulatory System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Sugadev, S. K. Burley, S. Swaminathan
Crystal Structure Of A Two-Component Response Regulator Fro Clostridium Difficile.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TWO-COMPONENT RESPONSE REGULATOR
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSGX3(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-126
    Gene: CD3265
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 6 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2QZJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Lys A:104 -Pro A:105
2Lys B:104 -Pro B:105
3Lys C:104 -Pro C:105
4Lys D:104 -Pro D:105
5Lys E:104 -Pro E:105
6Lys F:104 -Pro F:105

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2QZJ)

(-) 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:121
 aligned with Q180B0_PEPD6 | Q180B0 from UniProtKB/TrEMBL  Length:226

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         Q180B0_PEPD6     2 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMNS 122
               SCOP domains d2qzja_ A: automated matches                                                                                              SCOP domains
               CATH domains 2qzjA00 A:4-124  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeee.ee..eehhhhhhhhhh.....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qzj A   4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYmTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRmNS 124
                                    13        23        33        43        53        63        73       |83        93       103       113       123 
                                                                                                        81-MSE                                  122-MSE


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with Q180B0_PEPD6 | Q180B0 from UniProtKB/TrEMBL  Length:226

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         Q180B0_PEPD6     2 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMNS 122
               SCOP domains d2qzjb_ B: automated matches                                                                                              SCOP domains
               CATH domains 2qzjB00 B:4-124  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeee.ee..eehhhhhhhhh......eeeee...hhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qzj B   4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYmTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRmNS 124
                                    13        23        33        43        53        63        73       |83        93       103       113       123 
                                                                                                        81-MSE                                  122-MSE


Chain C from PDB  Type:PROTEIN  Length:121
 aligned with Q180B0_PEPD6 | Q180B0 from UniProtKB/TrEMBL  Length:226

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         Q180B0_PEPD6     2 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMNS 122
               SCOP domains d2qzjc_ C: automated matches                                                                                              SCOP domains
               CATH domains 2qzjC00 C:4-124  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh....eeee..ee..eehhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qzj C   4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYmTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRmNS 124
                                    13        23        33        43        53        63        73       |83        93       103       113       123 
                                                                                                        81-MSE                                  122-MSE


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with Q180B0_PEPD6 | Q180B0 from UniProtKB/TrEMBL  Length:226

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         Q180B0_PEPD6     2 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMNS 122
               SCOP domains d2qzjd_ D: automated matches                                                                                              SCOP domains
               CATH domains 2qzjD00 D:4-124  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qzj D   4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYmTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRmNS 124
                                    13        23        33        43        53        63        73       |83        93       103       113       123 
                                                                                                        81-MSE                                  122-MSE


Chain E from PDB  Type:PROTEIN  Length:121
 aligned with Q180B0_PEPD6 | Q180B0 from UniProtKB/TrEMBL  Length:226

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         Q180B0_PEPD6     2 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMNS 122
               SCOP domains d2qzje_ E: automated matches                                                                                              SCOP domains
               CATH domains 2qzjE00 E:4-124  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeee.ee..eehhhhhhhhhhhh...eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qzj E   4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYmTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRmNS 124
                                    13        23        33        43        53        63        73       |83        93       103       113       123 
                                                                                                        81-MSE                                  122-MSE


Chain F from PDB  Type:PROTEIN  Length:121
 aligned with Q180B0_PEPD6 | Q180B0 from UniProtKB/TrEMBL  Length:226

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
         Q180B0_PEPD6     2 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYMTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRMNS 122
               SCOP domains d2qzjf_ F: automated matches                                                                                              SCOP domains
               CATH domains 2qzjF00 F:4-124  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeee.......hhhhhhhhhhh.....eeeee...hhhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qzj F   4 QTKILIIDGDKDNCQKLKGFLEEKGISIDLAYNCEEAIGKIFSNKYDLIFLEIILSDGDGWTLCKKIRNVTTCPIVYmTYINEDQSILNALNSGGDDYLIKPLNLEILYAKVKAILRRmNS 124
                                    13        23        33        43        53        63        73       |83        93       103       113       123 
                                                                                                        81-MSE                                  122-MSE
   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  (1, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q180B0_PEPD6 | Q180B0)
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:0000160    phosphorelay signal transduction system    A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
    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.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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  Cis Peptide Bonds
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    Lys B:104 - Pro B:105   [ RasMol ]  
    Lys C:104 - Pro C:105   [ RasMol ]  
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  2qzj
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 Related Entries

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