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(-) Description

Title :  CRYSTAL STRUCTURE OF A REX-FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN FROM STREPTOCOCCUS AGALACTIAE COMPLEXED WITH NAD+
 
Authors :  S. Thiyagarajan, D. Logan, C. Von Wachenfeldt
Date :  26 Oct 09  (Deposition) - 10 Nov 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dna Binding Protein, Winged Helix, Rossmann Fold, Nad+, Repressor, Transcription, Transcription Regulation, Redox Sensing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Thiyagarajan, D. Logan, C. Von Wachenfeldt
Structure And Functional Properties Of The Streptococcus Agalactiae Transcriptional Repressor Rex
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET101
    Expression System Strain: TUNER (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GBS1167, REX
    Organism Scientific: STREPTOCOCCUS AGALACTIAE SEROGROUP III
    Organism Taxid: 216495
    Strain: NEM316

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MG7Ligand/IonMAGNESIUM ION
3NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:91 , CYS A:92 , GLY A:93 , ASN A:94 , ILE A:95 , ASP A:117 , LEU A:118 , ASN A:121 , ILE A:137 , THR A:155 , VAL A:156 , PRO A:157 , SER A:158 , VAL A:164 , PHE A:179 , SER A:180 , PRO A:181 , LEU A:197 , HOH A:225 , HOH A:235 , HOH A:309 , HOH A:371 , HOH A:374 , HOH A:396 , HOH A:402 , HOH A:423 , ALA B:98 , LEU B:99 , TYR B:102BINDING SITE FOR RESIDUE NAD A 213
02AC2SOFTWARETYR A:102 , ARG A:103 , NAD B:213 , HOH B:414BINDING SITE FOR RESIDUE MG A 214
03AC3SOFTWAREARG A:14 , HOH A:336 , ARG B:14BINDING SITE FOR RESIDUE MG A 215
04AC4SOFTWAREGLU A:77 , ARG A:212 , HOH A:512BINDING SITE FOR RESIDUE MG A 216
05AC5SOFTWAREHIS A:105 , ASP A:106 , HOH A:331BINDING SITE FOR RESIDUE MG A 217
06AC6SOFTWAREARG A:14 , HOH B:218 , HOH B:378BINDING SITE FOR RESIDUE CL A 218
07AC7SOFTWAREALA A:98 , LEU A:99 , TYR A:102 , MG A:214 , GLY B:91 , CYS B:92 , GLY B:93 , ASN B:94 , ILE B:95 , ASP B:117 , LEU B:118 , ILE B:137 , THR B:155 , VAL B:156 , PRO B:157 , SER B:158 , VAL B:164 , PHE B:179 , SER B:180 , PRO B:181 , LEU B:197 , HOH B:227 , HOH B:269 , HOH B:324 , HOH B:333 , HOH B:337 , HOH B:382 , HOH B:390 , HOH B:392 , HOH B:399 , HOH B:414BINDING SITE FOR RESIDUE NAD B 213
08AC8SOFTWAREGLN A:202 , ASP B:81 , HIS B:105 , MET B:110BINDING SITE FOR RESIDUE MG B 214
09AC9SOFTWARELEU A:42 , GLY A:43 , HOH A:355 , LYS B:13 , HOH B:288 , HOH B:411BINDING SITE FOR RESIDUE MG B 215
10BC1SOFTWAREASP B:119 , SER B:120 , HOH B:344BINDING SITE FOR RESIDUE MG B 216

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KEO)

(-) 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:206
 aligned with REX_STRA3 | Q8E565 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:207
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
            REX_STRA3     6 SIPKATAKRLSLYYRIFKRFNTDGIEKASSKQIADALGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNVMLVGCGNIGRALLHYRFHDRNKMQISMAFDLDSNDLVGKTTEDGIPVYGISTINDHLIDSDIETAILTVPSTEAQEVADILVKAGIKGILSFSPVHLTLPKDIIVQYVDLTSELQTLLYFMNQQR 212
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhhhhhhh.....eehhhhhhhhhhhh.....eeeeee..hhhhhhhh.........eeeeeeee................eee..hhhhhh-.....eeee..hhhhhhhhhhhhhhhh..eeee............eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3keo A   6 SIPKATAKRLSLYYRIFKRFNTDGIEKASSKQIADALGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNVMLVGCGNIGRALLHYRFHDRNKMQISMAFDLDSNDLVGKTTEDGIPVYGISTINDHL-DSDIETAILTVPSTEAQEVADILVKAGIKGILSFSPVHLTLPKDIIVQYVDLTSELQTLLYFMNQQR 212
                                    15        25        35        45        55        65        75        85        95       105       115       125       135        |-|      155       165       175       185       195       205       
                                                                                                                                                                    144 |                                                                  
                                                                                                                                                                      146                                                                  


Chain B from PDB  Type:PROTEIN  Length:207
 aligned with REX_STRA3 | Q8E565 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:207
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
            REX_STRA3     6 SIPKATAKRLSLYYRIFKRFNTDGIEKASSKQIADALGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNVMLVGCGNIGRALLHYRFHDRNKMQISMAFDLDSNDLVGKTTEDGIPVYGISTINDHLIDSDIETAILTVPSTEAQEVADILVKAGIKGILSFSPVHLTLPKDIIVQYVDLTSELQTLLYFMNQQR 212
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Put_DNA-bind_N-3keoB01 B:6-54                    ---------------------------CoA_binding-3keoB03 B:82-182                                                                         ------------------------------ Pfam domains (1)
           Pfam domains (2) Put_DNA-bind_N-3keoB02 B:6-54                    ---------------------------CoA_binding-3keoB04 B:82-182                                                                         ------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhh..........eehhhhhhhhhhhh.....eeeeee..hhhhhhhh.........eeeeeeee................eee..hhhhhhh.....eeee..hhhhhhhhhhhhhhhh..eeee............eeee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3keo B   6 SIPKATAKRLSLYYRIFKRFNTDGIEKASSKQIADALGIDSATVRRDFSYFGELGRRGFGYDVKKLMNFFAEILNDHSTTNVMLVGCGNIGRALLHYRFHDRNKMQISMAFDLDSNDLVGKTTEDGIPVYGISTINDHLIDSDIETAILTVPSTEAQEVADILVKAGIKGILSFSPVHLTLPKDIIVQYVDLTSELQTLLYFMNQQR 212
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205
   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 3KEO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KEO)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HTH (544)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (REX_STRA3 | Q8E565)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0050662    coenzyme binding    Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051775    response to redox state    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating redox state. Redox state refers to the balance of oxidized versus reduced forms of electron donors and acceptors in an organelle, cell or organ; plastoquinone, glutathione (GSH/GSSG), and nicotinamide nucleotides (NAD+/NADH and NADP+/NADPH) are among the most important.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        REX_STRA3 | Q8E565: 3keq 3ket

(-) Related Entries Specified in the PDB File

2dt5 CRYSTAL STRUCTURE OF TTHA1657 (AT-RICH DNA-BINDING PROTEIN) FROM THERMUS THERMOPHILUS HB8
2vt3 STRUCTURE AND FUNCTIONAL PROPERTIES OF THE BACILLUS SUBTILIS TRANSCRIPTIONAL REPRESSOR REX
3keq STRUCTURE AND FUNCTIONAL PROPERTIES OF THE STREPTOCOCCUS AGALACTIAE TRANSCRIPTIONAL REPRESSOR REX
3ket CRYSTAL STRUCTURE OF A REX-FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN FROM STREPTOCOCCUS AGALACTIAE BOUND TO A PALINDROMIC OPERATOR