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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF E. COLI TRANSCRIPTIONAL REGULATOR KDGR.
 
Authors :  A. Bochkarev, V. V. Lunin, A. Ezersky, E. Evdokimova, T. Skarina, X. Xu, A. Joachimiak, A. Savchenko, Midwest Center For Structural Geno (Mcsg)
Date :  08 Feb 05  (Deposition) - 22 Mar 05  (Release) - 05 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Transcriptional Regulator, Kdgr, Iclr, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bochkarev, V. V. Lunin, A. Ezersky, E. Evdokimova, T. Skarina, X. Xu D. Borek, A. Savchenko
Structural Study Of Effector Binding Specificity In Iclr Transcriptional Regulators
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTIONAL REGULATOR KDGR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: KDGR
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:9 , GLN A:10 , LYS A:165 , HOH A:212BINDING SITE FOR RESIDUE SO4 A 180

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YSP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YSP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric Unit
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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:164
 aligned with KDGR_ECOLI | P76268 from UniProtKB/Swiss-Prot  Length:263

    Alignment length:172
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256  
           KDGR_ECOLI    87 VDLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDSMYNLRMYSRIGRRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSISFPTLRFSEERLQEYVAMLHTAARKISAQMGY 258
               SCOP domains d1yspa_ A: automated matches                                                                                                                                                 SCOP domains
               CATH domains 1yspA00 A:1-172  [code=3.30.450.40, no na        me defined]                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------IclR-1yspA01 A:50-169                                                                                                   --- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeeee...--------...eee...hhhhhhhhhh.hhhhhhhhhh.............hhhhhhhhhhhhhhhh.eeee.......eeeeeeee.....eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ysp A   1 MDLIRSADIQMRELSRLTKETIHLGALDEDSIVYIHKIDSM--------IGRRNPLYSTAIGKVLLAWRDRDEVKQILEGVEYKRSTERTITSTEALLPVLDQVREQGYGEDNEEQEEGLRCIAVPVFDRFGVVIAGLSISFPTLRFSEERLQEYVAMLHTAARKISAQMGY 172
                                    10        20        30        40|       50        60        70        80        90       100       110       120       130       140       150       160       170  
                                                                   41       50
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: GAF (44)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (KDGR_ECOLI | P76268)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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