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(-) Description

Title :  CRYSTAL STRUCTURE OF SIGMA-54 INTERACTION DOMAIN PROTEIN FROM ENTEROCOCCUS FAECALIS
 
Authors :  C. Chang, A. Sather, K. Buck, A. Joachimiak, Midwest Center For Stru Genomics (Mcsg)
Date :  24 Feb 09  (Deposition) - 10 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Enterococcus Faecalis, Sigma-54 Interaction Domain Protein, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Atp-Binding, Nucleotide- Binding, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Chang, A. Sather, K. Buck, A. Joachimiak
Crystal Structure Of Sigma-54 Interaction Domain Protein From Enterococcus Faecalis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SIGMA-54 INTERACTION DOMAIN PROTEIN
    Atcc: 700802
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 544-679
    Gene: EF_1010
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: V583

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2MSE22Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3GDW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GDW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GDW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3GDW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3GDW)

(-) Exons   (0, 0)

(no "Exon" information available for 3GDW)

(-) 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:135
 aligned with Q836U6_ENTFA | Q836U6 from UniProtKB/TrEMBL  Length:901

    Alignment length:135
                                   550       560       570       580       590       600       610       620       630       640       650       660       670     
         Q836U6_ENTFA   541 PENNVGVFVLMHGDSTASSMLKTAQELLGTSIGTAMNMPLTMEVQTMYEQLRNQVITQKESLNNGILLLTDMGSLNSFGNMLFEETGIRTKAITMTSTMIVLEAIRMASVGRSLEDIYQNIQLSFESVVREQFRS 675
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3gdwA00 A:541-675  [code=3.40.50.510, no name defined]                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee..hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gdw A 541 SNANVGVFVLmHGDSTASSmLKTAQELLGTSIGTAmNmPLTmEVQTmYEQLRNQVITQKESLNNGILLLTDmGSLNSFGNmLFEETGIRTKAITmTSTmIVLEAIRmASVGRSLEDIYQNIQLSFESVVREQFRS 675
                                   550|      560       570     | 580 |    |590       600       610 |     620|      630    |  640      |650       660       670     
                                    551-MSE  560-MSE         576-MSE |    |                      612-MSE  621-MSE       635-MSE     647-MSE                        
                                                               578-MSE    |                                                 639-MSE                                
                                                                   582-MSE|                                                                                        
                                                                        587-MSE                                                                                    


Chain B from PDB  Type:PROTEIN  Length:138
 aligned with Q836U6_ENTFA | Q836U6 from UniProtKB/TrEMBL  Length:901

    Alignment length:138
                                   550       560       570       580       590       600       610       620       630       640       650       660       670        
         Q836U6_ENTFA   541 PENNVGVFVLMHGDSTASSMLKTAQELLGTSIGTAMNMPLTMEVQTMYEQLRNQVITQKESLNNGILLLTDMGSLNSFGNMLFEETGIRTKAITMTSTMIVLEAIRMASVGRSLEDIYQNIQLSFESVVREQFRSSLQ 678
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3gdwB00 B:541-678  [code=3.40.50.510, no name defined]                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeee..hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gdw B 541 SNANVGVFVLmHGDSTASSmLKTAQELLGTSIGTAmNmPLTmEVQTmYEQLRNQVITQKESLNNGILLLTDmGSLNSFGNmLFEETGIRTKAITmTSTmIVLEAIRmASVGRSLEDIYQNIQLSFESVVREQFRSSLQ 678
                                   550|      560       570     | 580 |    |590       600       610 |     620|      630    |  640      |650       660       670        
                                    551-MSE  560-MSE         576-MSE |    |                      612-MSE  621-MSE       635-MSE     647-MSE                           
                                                               578-MSE    |                                                 639-MSE                                   
                                                                   582-MSE|                                                                                           
                                                                        587-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  (0, 0)

(no "SCOP Domain" information available for 3GDW)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GDW)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q836U6_ENTFA | Q836U6)
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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0009401    phosphoenolpyruvate-dependent sugar phosphotransferase system    The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

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