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(-) Description

Title :  CRYSTAL STRUCTURE OF COLE7 TRANSLOCATION DOMAIN
 
Authors :  Y. S. Cheng, Z. Shi, L. G. Doudeva, W. Z. Yang, K. F. Chak, H. S. Yuan
Date :  04 Sep 05  (Deposition) - 14 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Colicin, Translocation Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. S. Cheng, Z. Shi, L. G. Doudeva, W. Z. Yang, K. F. Chak, H. S. Yuan
High-Resolution Crystal Structure Of A Truncated Cole7 Translocation Domain: Implications For Colicin Transport Across Membranes
J. Mol. Biol. V. 356 22 2006
PubMed-ID: 16360169  |  Reference-DOI: 10.1016/J.JMB.2005.11.056

(-) Compounds

Molecule 1 - COLICIN E7
    Chains: A
    EC Number: 3.1.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE70
    Expression System Strain: BL834 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL TRANSLOCATION DOMAIN
    Gene: COLE7 (AMINO ACIDS 60-316)
    Organism Scientific: ESCHERICHIA COLI STR. K12 SUBSTR.
    Organism Taxid: 316407
    Strain: W3110

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:162 , GLN A:163 , VAL A:164 , SER A:165 , ARG A:249 , HOH A:554 , HOH A:645 , HOH A:733 , HOH A:790BINDING SITE FOR RESIDUE SO4 A 402
2AC2SOFTWAREALA A:80 , ALA A:81 , MSE A:83 , ALA A:89 , ILE A:100 , SER A:101 , VAL A:151 , SER A:153 , HOH A:509 , HOH A:516BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AXC)

(-) Exons   (0, 0)

(no "Exon" information available for 2AXC)

(-) 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:232
 aligned with CEA7_ECOLX | Q47112 from UniProtKB/Swiss-Prot  Length:576

    Alignment length:236
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304      
           CEA7_ECOLX    75 SNSSVAAPMAFGFPALAAPGAGTLGISVSGEALSAAIADIFAALKGPFKFSAWGIALYGILPSEIAKDDPNMMSKIVTSLPAETVTNVQVSTLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPMSVPVVNAKPTRTPGVFHASFPGVPSLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPVYVSVTDVLTPAQVKQRQDEEKRLQQEWNDAHP 310
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eee......eeeee.....hhhhhhhhhh..----...eeeeeeeehhhhhhhhh.....eeeeeee.hhh...hhhhh.....eeee..eeeeeee..eeeeeeee...eeeeeee.ee.....eeeeee..eeeeeeee.............eee......ee........eeeeeee.hhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2axc A  75 SNSSVAAPmAFGFPALAAPGAGTLGISVSGEALSAAIADIFAALK----FSAWGIALYGILPSEIAKDDPNmmSKIVTSLPAETVTNVQVSTLPLDQATVSVTKRVTDVVKDTRQHIAVVAGVPmSVPVVNAKPTRTPGVFHASFPGVPSLTVSTVKGLPVSTTLPRGITEDKGRTAVPAGFTFGGGSHEAVIRFPKESGQKPVYVSVTDVLTPAQVKQRQDEEKRLQQEWNDAHP 310
                                    84        94       104       114    |  124       134       144 ||    154       164       174       184       194    |  204       214       224       234       244       254       264       274       284       294       304      
                                   83-MSE                             119  124                   146-MSE                                              199-MSE                                                                                                           
                                                                                                  147-MSE
   Legend:   → Mismatch (orange background)
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  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 2AXC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2AXC)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CEA7_ECOLX | Q47112)
molecular function
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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).
biological process
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005727    extrachromosomal circular DNA    Circular DNA structures that are not part of a chromosome.

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  CEA7_ECOLX | Q47112
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 Related Entries

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

UniProtKB/Swiss-Prot
        CEA7_ECOLX | Q47112: 1m08 1mz8 1pt3 1ujz 1zns 1znv 2erh 2ivh 2jaz 2jb0 2jbg 3fbd 3gjn 3gkl 3zfk 7cei

(-) Related Entries Specified in the PDB File

1m08 UNBOUNDED NUCLEASE DOMAIN OF COLE7
7cei THE DNASE DOMAIN OF COLE7 IN COMPLEX WITH IM7