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(-) Description

Title :  CRYSTAL STRUCTURE OF NTRC FAMILY TRANSCRIPTIONAL REGULATOR FROM CLOSTRIDIUM ACETOBUTYLICUM
 
Authors :  U. A. Ramagopal, M. Dickey, R. Toro, M. Iizuka, K. Groshong, L. Rodgers, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center Structural Genomics (Nysgxrc)
Date :  31 May 07  (Deposition) - 03 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  D  (1x)
Biol. Unit 3:  A,D  (1x)
Keywords :  Structural Genomics, Ntrc Family Transcriptional Regulator, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. A. Ramagopal, M. Dickey, R. Toro, M. Iizuka, K. Groshong, L. Rodgers J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Ntrc Family Transcriptional Regulator From Clostridium Acetobutylicum.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NTRC FAMILY TRANSCRIPTIONAL REGULATOR
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: BS-PSGX4(BC)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 2-186
    Gene: CA_C0459
    Organism Scientific: CLOSTRIDIUM ACETOBUTYLICUM ATCC 824
    Organism Taxid: 272562
    Strain: DSM 792, JCM 1419, LMG 5710, VKM B-1787
    Synonym: PAS AND AAA DOMAINS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AD
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  D
Biological Unit 3 (1x): AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric Unit (2, 15)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO411Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 3 (2, 15)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO411Ligand/IonSULFATE ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:0 , LEU A:1 , SER A:2 , ARG A:78 , HOH A:744 , HOH A:778 , ARG D:83 , GLY D:167 , GLU D:168 , GLU D:169 , HOH D:710 , HOH D:809BINDING SITE FOR RESIDUE SO4 A 601
02AC2SOFTWARELYS A:32 , GLU A:49 , LYS A:107 , HIS A:108 , HOH A:787BINDING SITE FOR RESIDUE SO4 A 602
03AC3SOFTWARETHR A:37 , TYR A:62 , SER A:125 , GLU A:126 , ASP A:127 , HOH A:836 , HOH A:882 , HOH D:776BINDING SITE FOR RESIDUE SO4 A 604
04AC4SOFTWARELYS A:32 , THR A:33 , HOH A:899BINDING SITE FOR RESIDUE SO4 A 606
05AC5SOFTWARELYS A:25 , ARG A:172 , HOH A:725 , HOH A:773BINDING SITE FOR RESIDUE SO4 A 608
06AC6SOFTWARELYS D:32 , GLU D:49 , LYS D:107 , HIS D:108 , HOH D:769BINDING SITE FOR RESIDUE SO4 D 603
07AC7SOFTWAREASN A:140 , TYR D:62 , SER D:125 , GLU D:126 , ASP D:127 , HOH D:821BINDING SITE FOR RESIDUE SO4 D 605
08AC8SOFTWARELYS D:32 , THR D:33 , HOH D:895BINDING SITE FOR RESIDUE SO4 D 607
09AC9SOFTWARELYS D:25 , ARG D:172 , HOH D:728 , HOH D:758 , HOH D:840BINDING SITE FOR RESIDUE SO4 D 609
10BC1SOFTWAREARG A:83 , GLY A:167 , GLU A:168 , GLU A:169 , HOH A:718 , HOH A:890 , SER D:0 , LEU D:1 , SER D:2 , ARG D:78 , HOH D:760 , HOH D:819BINDING SITE FOR RESIDUE SO4 D 610
11BC2SOFTWARETHR A:77 , ARG A:78 , PHE A:79 , THR D:77 , ARG D:78 , PHE D:79 , HOH D:804BINDING SITE FOR RESIDUE SO4 D 611
12BC3SOFTWARESER A:9 , GLN A:10 , ASN A:11 , ARG A:56 , GOL A:703 , HOH A:706 , HOH A:707 , HOH A:814 , HOH A:897BINDING SITE FOR RESIDUE GOL A 701
13BC4SOFTWAREGLN A:10 , ARG A:56 , ALA A:58 , THR A:59 , GLY A:147 , LYS A:148 , THR A:149 , VAL A:150 , GOL A:701 , HOH A:709BINDING SITE FOR RESIDUE GOL A 703
14BC5SOFTWARESER D:9 , GLN D:10 , ASN D:11 , LEU D:14 , ARG D:56 , GOL D:704 , HOH D:706 , HOH D:712 , HOH D:748 , HOH D:793BINDING SITE FOR RESIDUE GOL D 702
15BC6SOFTWAREGLN D:10 , ARG D:56 , ALA D:58 , THR D:59 , GLY D:147 , LYS D:148 , THR D:149 , VAL D:150 , GOL D:702 , HOH D:709BINDING SITE FOR RESIDUE GOL D 704

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q5C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Q5C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q5C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q5C)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q5C)

(-) 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:187
 aligned with Q97LU5_CLOAB | Q97LU5 from UniProtKB/TrEMBL  Length:627

    Alignment length:187
                             1                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       
         Q97LU5_CLOAB     - -MSLKIALISQNENLLNLFPKLALEKNFIPITKTASLTRASKIAFGLQDEVDAIISRGATSDYIKKSVSIPSISIKVTRFDTMRAVYNAKRFGNELALIAYKHSIVDKHEIEAMLGVKIKEFLFSSEDEITTLISKVKTENIKIVVSGKTVTDEAIKQGLYGETINSGEESLRRAIEEALNLIEVRN 186
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2q5cA01 A:0-75,A:166-186  [code=3.40.50.2300, no name defined]              2q5cA02 A:76-165 PrpR receptor domain-like                                                2q5cA01               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh....eeeeehhhhhhhhh.....eeee..hhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q5c A   0 SLSLKIALISQNENLLNLFPKLALEKNFIPITKTASLTRASKIAFGLQDEVDAIISRGATSDYIKKSVSIPSISIKVTRFDTMRAVYNAKRFGNELALIAYKHSIVDKHEIEAMLGVKIKEFLFSSEDEITTLISKVKTENIKIVVSGKTVTDEAIKQGLYGETINSGEESLRRAIEEALNLIEVRN 186
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       


Chain D from PDB  Type:PROTEIN  Length:187
 aligned with Q97LU5_CLOAB | Q97LU5 from UniProtKB/TrEMBL  Length:627

    Alignment length:187
                             1                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       
         Q97LU5_CLOAB     - -MSLKIALISQNENLLNLFPKLALEKNFIPITKTASLTRASKIAFGLQDEVDAIISRGATSDYIKKSVSIPSISIKVTRFDTMRAVYNAKRFGNELALIAYKHSIVDKHEIEAMLGVKIKEFLFSSEDEITTLISKVKTENIKIVVSGKTVTDEAIKQGLYGETINSGEESLRRAIEEALNLIEVRN 186
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2q5cD01 D:0-75,D:166-186  [code=3.40.50.2300, no name defined]              2q5cD02 D:76-165 PrpR receptor domain-like                                                2q5cD01               CATH domains
           Pfam domains (1) -------------------PrpR_N-2q5cD01 D:19-186                                                                                                                                                  Pfam domains (1)
           Pfam domains (2) -------------------PrpR_N-2q5cD02 D:19-186                                                                                                                                                  Pfam domains (2)
         Sec.struct. author ....eeeeee.hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhhhh....eeeeehhhhhhhhh.....eeee..hhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhh.eeeeeee.hhhhhhhhhhhhhhh...eeeehhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q5c D   0 SLSLKIALISQNENLLNLFPKLALEKNFIPITKTASLTRASKIAFGLQDEVDAIISRGATSDYIKKSVSIPSISIKVTRFDTMRAVYNAKRFGNELALIAYKHSIVDKHEIEAMLGVKIKEFLFSSEDEITTLISKVKTENIKIVVSGKTVTDEAIKQGLYGETINSGEESLRRAIEEALNLIEVRN 186
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   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 2Q5C)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: PrpR_N] (2)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,D   (Q97LU5_CLOAB | Q97LU5)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0000156    phosphorelay response regulator activity    Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
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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  2q5c
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