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(-) Description

Title :  STRUCTURE OF THE CITROBACTER FREUNDII EFFECTOR BINDING DOMAIN CONTAINING THREE AMINO ACID SUBSTITUTIONS: T103V, S221A AND Y264F
 
Authors :  B. L. Mark, M. D. Balcewich
Date :  13 Nov 09  (Deposition) - 26 May 10  (Release) - 28 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha-Beta-Sandwich, Activator, Dna-Binding, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. D. Balcewich, T. M. Reeve, E. A. Orlikow, L. J. Donald, D. J. Vocadlo, B. L. Mark
Crystal Structure Of The Ampr Effector Binding Domain Provides Insight Into The Molecular Regulation Of Inducible Ampc Beta-Lactamase.
J. Mol. Biol. V. 400 998 2010
PubMed-ID: 20594961  |  Reference-DOI: 10.1016/J.JMB.2010.05.040

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL ACTIVATOR AMPR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15A
    Expression System Strain: BL21 (DE3) GOLD HTE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 83-291, EFFECTOR BINDING DOMAIN
    Gene: AMPR
    Mutation: YES
    Organism Scientific: CITROBACTER FREUNDII
    Organism Taxid: 546

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1GOL10Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:148 , GLY A:149 , GLY A:150 , ALA A:151 , TRP A:152BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWARELEU A:184 , LYS A:185 , PHE A:186 , PRO A:187 , HIS A:213 , ASN A:214BINDING SITE FOR RESIDUE GOL A 2
3AC3SOFTWAREHOH A:31 , VAL A:103 , TYR A:147 , MET A:165 , PRO A:238 , HOH A:422 , HOH A:426BINDING SITE FOR RESIDUE GOL A 3
4AC4SOFTWAREPHE A:255 , LEU A:256 , THR A:257BINDING SITE FOR RESIDUE GOL A 4
5AC5SOFTWAREASP A:124 , LEU A:125 , HIS A:126 , HIS A:213 , ASN A:214 , VAL A:215BINDING SITE FOR RESIDUE GOL A 5

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KOT)

(-) 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:198
 aligned with AMPR_CITFR | P12529 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:198
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282        
           AMPR_CITFR    93 QEKLKIGVVGTFAIGCLFPLLSDFKRSYPHIDLHISTHNNRVDPAAEGLDYTIRYGGGAWHDTDAQYLCSALMSPLCSPTLASQIQTPADILKFPLLRSYRRDEWALWMQAAGEAPPSPTHNVMVFDSSVTMLEAAQGGMGVAIAPVRMFTHLLSSERIVQPFLTQIDLGSYWITRLQSRPETPAMREFSRWLTGVLH 290
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains LysR_substrate-3kotA01 A:93-290                                                                                                                                                                        Pfam domains
         Sec.struct. author .eeeeeee.hhhhh..hhhhhhhhhhhhh.eeeeeeee.....hhhh...eeeeee......eeeeeeeeeeeeeee.hhhhhhh..hhhhhh..eeee...hhhhhhhhhhh........eeeee.hhhhhhhhhhh...eeeeehhhhhhhhhh..............eeeeeee......hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3kot A  93 QEKLKIGVVGVFAIGCLFPLLSDFKRSYPHIDLHISTHNNRVDPAAEGLDYTIRYGGGAWHDTDAQYLCSALMSPLCSPTLASQIQTPADILKFPLLRSYRRDEWALWMQTVGEAPPSPTHNVMVFDSAVTMLEAAQAGMGVAIAPVRMFTHLLSSERIVQPFLTQIDLGSFWITRLQSRPETPAMREFSRWLTGVLH 290
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282
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  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 3KOT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMPR_CITFR | P12529)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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: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: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
        AMPR_CITFR | P12529: 3kos

(-) Related Entries Specified in the PDB File

3kos NATIVE AMPR STRUCTURE FROM CITROBACTER FREUNDII