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(-) Description

Title :  CRYSTAL STRUCTURE OF RSP IN COMPLEX WITH ALPHA-NAD+
 
Authors :  Y. Zheng, T. -P. Ko, R. -T. Guo
Date :  05 Aug 13  (Deposition) - 13 Aug 14  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Winged Helix, Rossmann Fold, Transcription Repressor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zheng, T. -P. Ko, Y. Yang, W. Shao, R. -T. Guo
Binding Mode Of The Oxidized Alpha-Anomer Of Nad(+) To Rsp, A Rex-Family Repressor
Biochem. Biophys. Res. Commun. V. 456 733 2015
PubMed-ID: 25527330  |  Reference-DOI: 10.1016/J.BBRC.2014.12.049

(-) Compounds

Molecule 1 - REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: REX, RSP
    Organism Scientific: THERMOANAEROBACTER ETHANOLICUS
    Organism Taxid: 509192
    Strain: JW200
    Synonym: RSP REPRESSOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
18NA2Ligand/IonALPHA-DIPHOSPHOPYRIDINE NUCLEOTIDE
2SO46Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:90 , GLY A:93 , ASN A:94 , LEU A:95 , ASP A:117 , ILE A:118 , ASN A:119 , CYS A:153 , ILE A:154 , PRO A:155 , ASN A:158 , THR A:162 , PHE A:177 , PRO A:179 , SO4 A:303 , HOH A:427 , HOH A:498 , HOH A:530 , HOH A:542 , HOH A:547 , HOH A:559 , ASN B:101 , TYR B:102 , THR B:103 , SER B:104BINDING SITE FOR RESIDUE 8NA A 301
2AC2SOFTWAREARG A:17 , ARG A:20 , TYR A:21 , HOH A:410 , ASN B:192 , HIS B:194BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREPRO A:179 , HIS A:194 , LEU A:195 , SER A:196 , 8NA A:301 , HOH A:408 , TYR B:102BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWARESER A:34 , SER A:35 , GLN A:61 , GLY A:63 , TYR A:64 , GLY A:65 , HOH A:520 , HOH A:521BINDING SITE FOR RESIDUE SO4 A 304
5AC5SOFTWAREGLN A:61 , ASN A:101 , TYR A:102 , THR A:103 , SER A:104 , HOH A:418 , ILE B:90 , GLY B:93 , ASN B:94 , LEU B:95 , ASP B:117 , ILE B:118 , ASN B:119 , LEU B:122 , CYS B:153 , ILE B:154 , PRO B:155 , PHE B:177 , PRO B:179 , SO4 B:302 , HOH B:451 , HOH B:453 , HOH B:454 , HOH B:455 , HOH B:456 , HOH B:464 , HOH B:538BINDING SITE FOR RESIDUE 8NA B 301
6AC6SOFTWARETYR A:102 , HIS B:194 , LEU B:195 , SER B:196 , 8NA B:301 , HOH B:449 , HOH B:483 , HOH B:617BINDING SITE FOR RESIDUE SO4 B 302
7AC7SOFTWARESER B:34 , SER B:35 , ARG B:36 , ARG B:50 , GLY B:65 , PRO B:185 , HOH B:411 , HOH B:559 , HOH B:594BINDING SITE FOR RESIDUE SO4 B 303
8AC8SOFTWAREHIS A:194 , ARG B:20 , HOH B:413 , HOH B:466BINDING SITE FOR RESIDUE SO4 B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WGG)

(-) 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:213
 aligned with D5KM69_THEET | D5KM69 from UniProtKB/TrEMBL  Length:224

    Alignment length:213
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   
         D5KM69_THEET     4 KTIVSMAVIRRLPRYHRYLEELLKNDVKRISSRELSEKMGVTASQIRQDLNNFGGFGQQGYGYNVEELYNNLTKILGLDKTYNTIIIGAGNLGQAIANYTSFEKSGFNLKGIFDINPRLFGLKIRDVEVMDVETVEDFIARNKIDIGILCIPKDNAQYTADRLVRAGIKAIWNFLPIDLKVPDDVILENVHLSDSLFTVSYRLNEEELFKKLK 216
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhh..........eehhhhhhhhhhhh.....eeeeee..hhhhhhhhh.hhhhhh.eeeeeeee.hhhhh..ee..eeeee..hhhhhhhhh...eeee..hhhhhhhhhhhhhhh...eeee............eeee..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wgg A   4 KTIVSMAVIRRLPRYHRYLEELLKNDVKRISSRELSEKMGVTASQIRQDLNNFGGFGQQGYGYNVEELYNNLTKILGLDKTYNTIIIGAGNLGQAIANYTSFEKSGFNLKGIFDINPRLFGLKIRDVEVMDVETVEDFIARNKIDIGILCIPKDNAQYTADRLVRAGIKAIWNFLPIDLKVPDDVILENVHLSDSLFTVSYRLNEEELFKKLK 216
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   


Chain B from PDB  Type:PROTEIN  Length:213
 aligned with D5KM69_THEET | D5KM69 from UniProtKB/TrEMBL  Length:224

    Alignment length:213
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213   
         D5KM69_THEET     4 KTIVSMAVIRRLPRYHRYLEELLKNDVKRISSRELSEKMGVTASQIRQDLNNFGGFGQQGYGYNVEELYNNLTKILGLDKTYNTIIIGAGNLGQAIANYTSFEKSGFNLKGIFDINPRLFGLKIRDVEVMDVETVEDFIARNKIDIGILCIPKDNAQYTADRLVRAGIKAIWNFLPIDLKVPDDVILENVHLSDSLFTVSYRLNEEELFKKLK 216
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhh.hhhhhhhhhhh..........eehhhhhhhhhhhh.....eeeeee..hhhhhhhhh.hhhhhh.eeeeeeee.hhhhh..ee..eeeee..hhhhhhhhh...eeee..hhhhhhhhhhhhhhh...eeee............eeee..hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wgg B   4 KTIVSMAVIRRLPRYHRYLEELLKNDVKRISSRELSEKMGVTASQIRQDLNNFGGFGQQGYGYNVEELYNNLTKILGLDKTYNTIIIGAGNLGQAIANYTSFEKSGFNLKGIFDINPRLFGLKIRDVEVMDVETVEDFIARNKIDIGILCIPKDNAQYTADRLVRAGIKAIWNFLPIDLKVPDDVILENVHLSDSLFTVSYRLNEEELFKKLK 216
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213
   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 3WGG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (D5KM69_THEET | D5KM69)
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: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: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/TrEMBL
        D5KM69_THEET | D5KM69: 3wg9 3wgh 3wgi

(-) Related Entries Specified in the PDB File

3wg9 NATIVE PROTEIN
3wgh SAME PROTEIN IN COMPLEX WITH BETA-NADH
3wgi SAME PROTEIN IN COMPLEX WITH BETA-NAD+ AND OPERATOR DNA