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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BACTERIAL ANTITOXIN HIGA FROM ESCHERICHIA COLI AT PH 8.5. NORTHEAST STRUCTURAL GENOMICS TARGET ER390.
 
Authors :  M. A. Arbing, M. Abashidze, J. M. Hurley, L. Zhao, H. Janjua, K. Cunningh L. C. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, M. Inouye, N. A G. T. Montelione, J. F. Hunt, Northeast Structural Genomics Conso (Nesg)
Date :  13 Sep 06  (Deposition) - 26 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Helix-Turn-Helix, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Arbing, S. K. Handelman, A. P. Kuzin, G. Verdon, C. Wang, M. Su, F. P. Rothenbacher, M. Abashidze, M. Liu, J. M. Hurley, R. Xiao, T. Acton, M. Inouye, G. T. Montelione, N. A. Woychik, J. F. Hunt
Crystal Structures Of Phd-Doc, Higa, And Yeeu Establish Multiple Evolutionary Links Between Microbial Growth-Regulating Toxin-Antitoxin Systems.
Structure V. 18 996 2010
PubMed-ID: 20696400  |  Reference-DOI: 10.1016/J.STR.2010.04.018

(-) Compounds

Molecule 1 - ANTITOXIN HIGA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-HIGA
    Expression System Strain: BL21(DE3)+ MAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HIGA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 199310
    Strain: CFT073
    Synonym: PUTATIVE HTH-TYPE TRANSCRIPTIONAL REGULATOR YDDM

 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, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2ICT)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ICT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ICT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ICT)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.YDDM_ECOL613-67  1A:13-67
YDDM_ECOLI13-67  1A:13-67
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.YDDM_ECOL613-67  1A:13-67
YDDM_ECOLI13-67  1A:13-67
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_CROC1PS50943 Cro/C1-type HTH domain profile.YDDM_ECOL613-67  2A:13-67
YDDM_ECOLI13-67  2A:13-67

(-) Exons   (0, 0)

(no "Exon" information available for 2ICT)

(-) 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:94
 aligned with YDDM_ECOL6 | P67700 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
            YDDM_ECOL6    1 MKMANHPRPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQNAWSLAEAEKTVDVSRLRRLVTQ 94
               SCOP domains d2icta_ A: Antitoxin HigA                                                                      SCOP domains
               CATH domains -2ictA01 A:2-82 lambda repressor-like DNA-binding domains                         ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ------------HTH_CROC1  PDB: A:13-67 UniProt: 13-67                 --------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  2ict A  1 mKmANHPRPGDIIQESLDELNVSLREFARAmEIAPSTASRLLTGKAALTPEmAIKLSVVIGSSPQmWLNLQNAWSLAEAEKTVDVSRLRRLVTQ 94
                            | |     10        20        30|       40        50 |      60     |  70        80        90    
                            | |                          31-MSE               52-MSE        66-MSE                        
                            1-MSE                                                                                         
                              3-MSE                                                                                       


Chain A from PDB  Type:PROTEIN  Length:94
 aligned with YDDM_ECOLI | P67699 from UniProtKB/Swiss-Prot  Length:94

    Alignment length:94
                                    10        20        30        40        50        60        70        80        90    
            YDDM_ECOLI    1 MKMANHPRPGDIIQESLDELNVSLREFARAMEIAPSTASRLLTGKAALTPEMAIKLSVVIGSSPQMWLNLQNAWSLAEAEKTVDVSRLRRLVTQ 94
               SCOP domains d2icta_ A: Antitoxin HigA                                                                      SCOP domains
               CATH domains -2ictA01 A:2-82 lambda repressor-like DNA-binding domains                         ------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------HTH_CROC1  PDB: A:13-67 UniProt: 13-67                 --------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  2ict A  1 mKmANHPRPGDIIQESLDELNVSLREFARAmEIAPSTASRLLTGKAALTPEmAIKLSVVIGSSPQmWLNLQNAWSLAEAEKTVDVSRLRRLVTQ 94
                            | |     10        20        30|       40        50 |      60     |  70        80        90    
                            1-MSE                        31-MSE               52-MSE        66-MSE                        
                              3-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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ICT)

(-) Gene Ontology  (4, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (YDDM_ECOL6 | P67700)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
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.

Chain A   (YDDM_ECOLI | P67699)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
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.

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  2ict
    Family and Domain Information: ProDom | SYSTERS
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  YDDM_ECOL6 | P67700
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  YDDM_ECOLI | P67699
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 Related Entries

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

UniProtKB/Swiss-Prot
        YDDM_ECOL6 | P67700: 2icp
        YDDM_ECOLI | P67699: 2icp

(-) Related Entries Specified in the PDB File

2icp CRYSTAL STRUCTURE OF THE BACTERIAL ANTITOXIN HIGA FROM ESCHERICHIA COLI AT PH 4.0 RELATED ID: ER390 RELATED DB: TARGETDB