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(-) Description

Title :  IDENTIFICATION OF THE GLYCAN TARGET OF THE NEMATOTOXIC FUNGAL GALECTIN CGL2 IN CAENORHABDITIS ELEGANS
 
Authors :  A. Butschi, A. Titz, M. Waelti, V. Olieric, K. Paschinger, G. Xiaoqiang, P. H. Seeberger, I. B. H. Wilson, M. Aebi, M. O. Hengartner, M. Kuenzler
Date :  14 Jun 09  (Deposition) - 19 Jan 10  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Sugar-Binding Protein, Lectin, Galectin, Secreted, Cell Wall, Sugar Binding, Sugar Binding Protein, Beta-Galactoside Binding Lectin, Fruiting Body, Extracellular Matrix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Butschi, A. Titz, M. A. Walti, V. Olieric, K. Paschinger, K. Nobauer, X. Guo, P. H. Seeberger, I. B. H. Wilson, M. Aebi, M. O. Hengartner, M. Kunzler
Caenorhabditis Elegans N-Glycan Core Beta- Galactoside Confers Sensitivity Towards Nematotoxic Fungal Galectin Cgl2.
Plos Pathog. V. 6 E717 2010
PubMed-ID: 20062796  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1000717

(-) Compounds

Molecule 1 - GALECTIN-2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: COPRINOPSIS CINEREA
    Organism Taxid: 5346
    Synonym: GALECTIN CGL2, GALECTIN II , CGL-II

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1FUC4Ligand/IonALPHA-L-FUCOSE
2GAL4Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4MG1Ligand/IonMAGNESIUM ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS D:51 , ARG D:55 , ASN D:64 , TRP D:72 , GLU D:75 , FUC D:1152 , HOH D:2089 , HOH D:2200BINDING SITE FOR RESIDUE GAL D1151
2AC2SOFTWAREHOH C:2075 , ARG D:55 , GLU D:75 , GAL D:1151BINDING SITE FOR RESIDUE FUC D1152
3AC3SOFTWAREARG A:55 , GLU A:75 , ARG A:77 , GAL A:1152BINDING SITE FOR RESIDUE FUC A1151
4AC4SOFTWAREHIS A:51 , SER A:53 , ARG A:55 , ASN A:64 , TRP A:72 , GLU A:75 , FUC A:1151 , HOH A:2095 , HOH A:2213 , HOH A:2214 , HOH A:2215 , HOH A:2216BINDING SITE FOR RESIDUE GAL A1152
5AC5SOFTWAREASN D:8BINDING SITE FOR RESIDUE MG C1155
6AC6SOFTWAREGLU A:58 , ASN A:59 , PRO A:79 , ARG C:85 , PRO C:86 , HOH C:2192 , HOH C:2194BINDING SITE FOR RESIDUE GOL C1154
7AC7SOFTWAREASN A:8 , ASN A:129 , HOH A:2012 , HOH A:2187 , HOH A:2188 , HIS B:51 , ARG B:55 , ASN B:64 , TRP B:72 , GLU B:75 , ARG B:77 , HOH B:2087 , HOH B:2205 , HOH B:2207 , HOH B:2208BINDING SITE FOR CHAIN B OF RESIDUES 1151 TO 1153
8AC8SOFTWAREPHE C:6 , HIS C:51 , ARG C:55 , GLU C:58 , ASN C:64 , GLU C:75 , ARG C:77 , HOH C:2084 , HOH C:2189 , HOH C:2190 , HOH C:2191 , PHE D:6 , ASN D:9 , SER D:134 , HOH D:2011 , HOH D:2014 , HOH D:2180BINDING SITE FOR CHAIN C OF RESIDUES 1151 TO 1153

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Pro A:86 -Pro A:87
2Ser A:134 -Pro A:135
3Pro B:86 -Pro B:87
4Ser B:134 -Pro B:135
5Pro C:86 -Pro C:87
6Ser C:134 -Pro C:135
7Pro D:86 -Pro D:87
8Ser D:134 -Pro D:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.CGL2_COPCI9-141
 
 
 		  4A:9-141
B:9-141
C:9-141
D:9-141

(-) Exons   (0, 0)

(no "Exon" information available for 2WKK)

(-) 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:150
 aligned with CGL2_COPCI | Q9P4R8 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           CGL2_COPCI     1 MLYHLFVNNQVKLQNDFKPESVAAIRSSAFNSKGGTTVFNFLSAGENILLHISIRPGENVIVFNSRLKNGAWGPEERIPYAEKFRPPNPSITVIDHGDRFQIRFDYGTSIYYNKRIKENAAAIAYNAENSLFSSPVTVDVHGLLPPLPPA 150
               SCOP domains d2wkka_ A: automated matches                                                                                                                           SCOP domains
               CATH domains 2wkkA00 A:1-150  [code=2.60.120.200, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eeeeeeeee....eeeee..........eeeeee.....eeeeeeee....eeeeeee.........eeee..........eeeeee...eeeee......eeee......eeeeeeee........eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GALECTIN  PDB: A:9-141 UniProt: 9-141                                                                                                --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wkk A   1 MLYHLFVNNQVKLQNDFKPESVAAIRSSAFNSKGGTTVFNFLSAGENILLHISIRPGENVIVFNSRLKNGAWGPEERIPYAEKFRPPNPSITVIDHGDRFQIRFDYGTSIYYNKRIKENAAAIAYNAENSLFSSPVTVDVHGLLPPLPPA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain B from PDB  Type:PROTEIN  Length:150
 aligned with CGL2_COPCI | Q9P4R8 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           CGL2_COPCI     1 MLYHLFVNNQVKLQNDFKPESVAAIRSSAFNSKGGTTVFNFLSAGENILLHISIRPGENVIVFNSRLKNGAWGPEERIPYAEKFRPPNPSITVIDHGDRFQIRFDYGTSIYYNKRIKENAAAIAYNAENSLFSSPVTVDVHGLLPPLPPA 150
               SCOP domains d2wkkb_ B: automated matches                                                                                                                           SCOP domains
               CATH domains 2wkkB00 B:1-150  [code=2.60.120.200, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eeeeeeeee....eeeee..........eeeeee.....eeeeeeeehhh.eeeeeee.........eeee..........eeeeee...eeeee......eeee......eeeeeee.........eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GALECTIN  PDB: B:9-141 UniProt: 9-141                                                                                                --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wkk B   1 MLYHLFVNNQVKLQNDFKPESVAAIRSSAFNSKGGTTVFNFLSAGENILLHISIRPGENVIVFNSRLKNGAWGPEERIPYAEKFRPPNPSITVIDHGDRFQIRFDYGTSIYYNKRIKENAAAIAYNAENSLFSSPVTVDVHGLLPPLPPA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain C from PDB  Type:PROTEIN  Length:150
 aligned with CGL2_COPCI | Q9P4R8 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           CGL2_COPCI     1 MLYHLFVNNQVKLQNDFKPESVAAIRSSAFNSKGGTTVFNFLSAGENILLHISIRPGENVIVFNSRLKNGAWGPEERIPYAEKFRPPNPSITVIDHGDRFQIRFDYGTSIYYNKRIKENAAAIAYNAENSLFSSPVTVDVHGLLPPLPPA 150
               SCOP domains d2wkkc_ C: automated matches                                                                                                                           SCOP domains
               CATH domains 2wkkC00 C:1-150  [code=2.60.120.200, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee...eeeeeeeee....eeeee..........eeeeee.....eeeeeeee....eeeeeee.........eeee..........eeeeee...eeeee......eeee......eeeeeeee........eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GALECTIN  PDB: C:9-141 UniProt: 9-141                                                                                                --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wkk C   1 MLYHLFVNNQVKLQNDFKPESVAAIRSSAFNSKGGTTVFNFLSAGENILLHISIRPGENVIVFNSRLKNGAWGPEERIPYAEKFRPPNPSITVIDHGDRFQIRFDYGTSIYYNKRIKENAAAIAYNAENSLFSSPVTVDVHGLLPPLPPA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150


Chain D from PDB  Type:PROTEIN  Length:150
 aligned with CGL2_COPCI | Q9P4R8 from UniProtKB/Swiss-Prot  Length:150

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           CGL2_COPCI     1 MLYHLFVNNQVKLQNDFKPESVAAIRSSAFNSKGGTTVFNFLSAGENILLHISIRPGENVIVFNSRLKNGAWGPEERIPYAEKFRPPNPSITVIDHGDRFQIRFDYGTSIYYNKRIKENAAAIAYNAENSLFSSPVTVDVHGLLPPLPPA 150
               SCOP domains d2wkkd_ D: automated matches                                                                                                                           SCOP domains
               CATH domains 2wkkD00 D:1-150  [code=2.60.120.200, no name defined]                                                                                                  CATH domains
           Pfam domains (1) -------Gal-bind_lectin-2wkkD01 D:8-134                                                                                                ---------------- Pfam domains (1)
           Pfam domains (2) -------Gal-bind_lectin-2wkkD02 D:8-134                                                                                                ---------------- Pfam domains (2)
           Pfam domains (3) -------Gal-bind_lectin-2wkkD03 D:8-134                                                                                                ---------------- Pfam domains (3)
           Pfam domains (4) -------Gal-bind_lectin-2wkkD04 D:8-134                                                                                                ---------------- Pfam domains (4)
         Sec.struct. author .eeee...eeeeeeeee....eeeee..........eeeeee.....eeeeeeeehhh.eeeeeee.........eeee..........eeeeee...eeeee......eeee......eeeeeeee........eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------GALECTIN  PDB: D:9-141 UniProt: 9-141                                                                                                --------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wkk D   1 MLYHLFVNNQVKLQNDFKPESVAAIRSSAFNSKGGTTVFNFLSAGENILLHISIRPGENVIVFNSRLKNGAWGPEERIPYAEKFRPPNPSITVIDHGDRFQIRFDYGTSIYYNKRIKENAAAIAYNAENSLFSSPVTVDVHGLLPPLPPA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (CGL2_COPCI | Q9P4R8)
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.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    GO:0012505    endomembrane system    A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CGL2_COPCI | Q9P4R8: 1ul9 1ulc 1uld 1ule 1ulf 1ulg

(-) Related Entries Specified in the PDB File

1ul9 CGL2 LIGANDFREE
1ulc CGL2 IN COMPLEX WITH LACTOSE
1uld CGL2 IN COMPLEX WITH BLOOD GROUP H TYPE II
1ule CGL2 IN COMPLEX WITH LINEAR B2 TRISACCHARIDE
1ulf CGL2 IN COMPLEX WITH BLOOD GROUP A TETRASACCHARIDE
1ulg CGL2 IN COMPLEX WITH THOMSEN-FRIEDENREICH ANTIGEN