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(-) Description

Title :  GAFD (F17C-TYPE) FIMBRIAL ADHESIN FROM ESCHERICHIA COLI
 
Authors :  M. C. Merckel, J. Tanskanen, S. Edelman, B. Westerlund-Wikstrom, T. K. Korhonen, A. Goldman
Date :  22 Jun 03  (Deposition) - 15 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lectin, Adhesin, N-Acetyl-D-Glucosamine Binding, Glcnac Binding Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Merckel, J. Tanskanen, S. Edelman, B. Westerlund-Wikstrom, T. K. Korhonen, A. Goldman
The Structural Basis Of Receptor-Binding By Escherichia Coli Associated With Diarrhea And Septicemia
J. Mol. Biol. V. 331 897 2003
PubMed-ID: 12909017  |  Reference-DOI: 10.1016/S0022-2836(03)00841-6

(-) Compounds

Molecule 1 - FIMBRIAL LECTIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGAFD(1-178)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-22B(+)
    Fragment: LIGAND-BINDING DOMAIN, RESIDUES 23-200
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: 2 NAG (GLCNAC) MOLECULES PER MONOMER DISULPHIDE BETWEEN C53 AND C110
    Other Details - Source: RESIDUES 1-178
    Strain: ETEC STRAINS
    Synonym: GAFD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:43 , ASN A:44 , ASP A:88 , THR A:89 , ARG A:93 , TRP A:109 , THR A:117 , GLN A:118 , GLY A:119 , HOH A:2080 , HOH A:2124BINDING SITE FOR RESIDUE NAG A 201
2AC2SOFTWARESER A:20 , ASP A:57 , TRP A:102 , ASN A:104 , ALA A:135 , GLN A:136 , ARG A:148 , ARG A:150 , ASN A:174 , ASP A:175 , THR A:176 , HOH A:2073 , HOH A:2125BINDING SITE FOR RESIDUE NAG A 202
3AC3SOFTWAREALA B:43 , ASN B:44 , ASP B:88 , THR B:89 , TRP B:109 , THR B:117 , GLN B:118 , GLY B:119 , HOH B:2108 , HOH B:2109 , HOH B:2110 , HOH B:2111BINDING SITE FOR RESIDUE NAG B 201
4AC4SOFTWAREASP B:57 , TRP B:102 , ASN B:104 , ALA B:135 , GLN B:136 , ARG B:148 , ARG B:150 , ASN B:174 , ASP B:175 , THR B:176BINDING SITE FOR RESIDUE NAG B 202

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:53 -A:110
2B:53 -B:110

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:28 -Pro A:29
2Leu B:28 -Pro B:29

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OIO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OIO)

(-) Exons   (0, 0)

(no "Exon" information available for 1OIO)

(-) 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:178
 aligned with F17GG_ECOLX | Q47341 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:178
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        
          F17GG_ECOLX    23 AVSFIGSTENDVGPSQGSYSSTHAMDNLPFVYNTGYNIGYQNANVWRISGGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGDTNYSRGTAMSGNSWENVFSGWCVGNYVSTQGLSVHVRPVILKRNSSAQYSVQKTSIGSIRMRPYNGSSAGSVQTTVNFSLNPFTLNDTVT 200
               SCOP domains d1oioa_ A: Fimbrial lectin GafD                                                                                                                                                    SCOP domains
               CATH domains 1oioA00 A:1-178 Bacterial adhesins - F17c-type                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeee....eeeeeeee.....ee.......eeeeeeeeeee...eeeeeeee...................eeeeeeee..hhh..........eeeeeeee....eeeeeeeeeeeeee......eeeee..eeeeeeeeee...........eeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oio A   1 AVSFIGSTENDVGPSQGSYSSTHAMDNLPFVYNTGYNIGYQNANVWRISGGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGDTNYSRGTAMSGNSWENVFSGWCVGNYVSTQGLSVHVRPVILKRNSSAQYSVQKTSIGSIRMRPYNGSSAGSVQTTVNFSLNPFTLNDTVT 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170        


Chain B from PDB  Type:PROTEIN  Length:178
 aligned with F17GG_ECOLX | Q47341 from UniProtKB/Swiss-Prot  Length:343

    Alignment length:178
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        
          F17GG_ECOLX    23 AVSFIGSTENDVGPSQGSYSSTHAMDNLPFVYNTGYNIGYQNANVWRISGGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGDTNYSRGTAMSGNSWENVFSGWCVGNYVSTQGLSVHVRPVILKRNSSAQYSVQKTSIGSIRMRPYNGSSAGSVQTTVNFSLNPFTLNDTVT 200
               SCOP domains d1oiob_ B: Fimbrial lectin GafD                                                                                                                                                    SCOP domains
               CATH domains 1oioB00 B:1-178 Bacterial adhesins - F17c-type                                                                                                                                     CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------Fimbrial-1oioB01  Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------Fimbrial-1oioB02  Pfam domains (2)
           Pfam domains (3) -Fim-adh_lectin-1oioB03 B:2-171                                                                                                                                            ------- Pfam domains (3)
           Pfam domains (4) -Fim-adh_lectin-1oioB04 B:2-171                                                                                                                                            ------- Pfam domains (4)
         Sec.struct. author .eee....eeee....eeeeeeee.....ee.......eeeeeeeeee....eeeeeeee...................eeeeeeee..hhhhh........eeeeeeee.....eeeeeeeeeeeee......eeeee..eeeeeeeeee...........eeeeee..eeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oio B   1 AVSFIGSTENDVGPSQGSYSSTHAMDNLPFVYNTGYNIGYQNANVWRISGGFCVGLDGKVDLPVVGSLDGQSIYGLTEEVGLLIWMGDTNYSRGTAMSGNSWENVFSGWCVGNYVSTQGLSVHVRPVILKRNSSAQYSVQKTSIGSIRMRPYNGSSAGSVQTTVNFSLNPFTLNDTVT 178
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: Adhesin (36)
(-)
Clan: no clan defined [family: Fim-adh_lectin] (6)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (F17GG_ECOLX | Q47341)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
biological process
    GO:0044406    adhesion of symbiont to host    The attachment of a symbiont to its host via adhesion molecules, general stickiness etc., either directly or indirectly. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    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:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

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