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(-) Description

Title :  STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH GALACTOSE BETA 1-3 GALNAC AT 1.8 A RESOLUTION.
 
Authors :  S. Mathieu, A. Imberty, A. Varrot
Date :  07 Jul 09  (Deposition) - 26 May 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Type-H Lectin, Cell Adhesion, Discoidin Domain, Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mathieu, K. Saboia Aragao, A. Imberty, A. Varrot
Discoidin I From Dictyostelium Discoideum And Interactions With Oligosaccharides: Specificity, Affinity, Crystal Structures And Comparison With Discoidin Ii.
J. Mol. Biol. V. 400 540 2010
PubMed-ID: 20580724  |  Reference-DOI: 10.1016/J.JMB.2010.05.042

(-) Compounds

Molecule 1 - DISCOIDIN-1 SUBUNIT A
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX-HTB
    Expression System Strain: ROSETTA 2 (DE3) PLYSS
    Expression System Taxid: 562
    Organism Common: SLIME MOLD
    Organism Scientific: DICTYOSTELIUM DISCOIDEUM
    Organism Taxid: 366501
    Strain: AX2
    Synonym: DISCOIDIN-1 SUBUNIT ALPHA, DISCOIDIN I CHAIN A

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 22)

Asymmetric/Biological Unit (7, 22)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2A2G3Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
3CA3Ligand/IonCALCIUM ION
4GAL3Ligand/IonBETA-D-GALACTOSE
5GOL8Ligand/IonGLYCEROL
6NGA3Ligand/IonN-ACETYL-D-GALACTOSAMINE
7SO41Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:164 , ASP A:203 , ASP A:246 , GLN B:219 , HOH B:2299 , HOH B:2300BINDING SITE FOR RESIDUE CA A 400
02AC2SOFTWARESER A:157 , THR A:159 , SER B:157 , VAL B:158 , THR B:159 , SER C:157 , THR C:159BINDING SITE FOR RESIDUE SO4 A 401
03AC3SOFTWAREARG A:104 , VAL A:109 , THR A:110 , HIS A:121BINDING SITE FOR RESIDUE GOL A 500
04AC4SOFTWARETYR A:23 , HIS A:27 , CYS A:51 , ARG A:79 , GLN A:84 , HOH A:2383 , THR B:41 , ASN B:42BINDING SITE FOR RESIDUE GOL A 501
05AC5SOFTWAREARG A:18 , TYR A:60 , LYS A:90 , ARG A:92 , TRP A:100 , GLU A:102 , HIS A:135 , HOH A:2172 , HOH A:2277 , HOH A:2384 , GLN C:8 , ALA C:11BINDING SITE FOR RESIDUE 1PG A 502
06AC6SOFTWAREASP B:164 , ASP B:203 , ASP B:246 , GLN C:219 , HOH C:2270 , HOH C:2271BINDING SITE FOR RESIDUE CA B 400
07AC7SOFTWAREARG B:104 , VAL B:109 , THR B:110 , HOH B:2361 , HOH B:2362BINDING SITE FOR RESIDUE GOL B 500
08AC8SOFTWARETHR A:41 , ASN A:42 , HOH A:2093 , TYR B:23 , HIS B:27 , CYS B:51 , ARG B:79 , GLN B:84BINDING SITE FOR RESIDUE GOL B 501
09AC9SOFTWAREALA A:11 , ARG B:18 , VAL B:62 , ALA B:133 , HIS B:135 , HOH B:2363BINDING SITE FOR RESIDUE GOL B 502
10BC1SOFTWAREGLN A:219 , HOH A:2321 , HOH A:2322 , ASP C:164 , ASP C:203 , ASP C:246BINDING SITE FOR RESIDUE CA C 400
11BC2SOFTWAREARG C:104 , THR C:110 , HIS C:121 , HOH C:2332 , HOH C:2333BINDING SITE FOR RESIDUE GOL C 500
12BC3SOFTWARETYR C:23 , HIS C:27 , THR C:41 , ASN C:42 , ARG C:79 , GLN C:84 , HIS C:142BINDING SITE FOR RESIDUE GOL C 501
13BC4SOFTWAREALA B:11 , ARG C:18 , ARG C:92 , ALA C:133 , HIS C:135BINDING SITE FOR RESIDUE GOL C 502
14BC5SOFTWARETYR A:166 , ASP A:206 , TYR A:241 , SER A:242 , HOH A:2324 , HOH A:2373 , HOH A:2374 , HOH A:2375 , HOH A:2376 , HOH A:2377 , HOH A:2378 , HOH A:2379 , HOH A:2381 , HOH A:2382 , GLN B:213 , ARG B:215 , TRP B:235 , ASN B:236BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 300 TO 302
15BC6SOFTWARETYR B:166 , GLN B:204 , ASP B:206 , TYR B:241 , SER B:242 , HOH B:2350 , HOH B:2351 , HOH B:2352 , HOH B:2353 , HOH B:2354 , HOH B:2355 , HOH B:2356 , HOH B:2357 , HOH B:2358 , HOH B:2359 , HOH B:2360 , GLN C:213 , ARG C:215 , TRP C:235 , ASN C:236BINDING SITE FOR CHAIN B OF POLYSACCHARIDE RESIDUES 300 TO 302
16BC7SOFTWAREARG A:215 , TRP A:235 , ASN A:236 , TYR C:166 , GLN C:204 , ASP C:206 , TYR C:241 , SER C:242 , HOH C:2273 , HOH C:2325 , HOH C:2326 , HOH C:2328 , HOH C:2329 , HOH C:2330 , HOH C:2331BINDING SITE FOR CHAIN C OF POLYSACCHARIDE RESIDUES 300 TO 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WN2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WN2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WN2)

(-) PROSITE Motifs  (2, 5)

Asymmetric/Biological Unit (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.DIS1A_DICDI1-152
 		  2A:1-152
C:1-152
2FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.DIS1A_DICDI49-78
 
 		  3A:49-78
B:49-78
C:49-78

(-) Exons   (0, 0)

(no "Exon" information available for 2WN2)

(-) 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:254
 aligned with DIS1A_DICDI | P02886 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:254
                             1                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    
          DIS1A_DICDI     - -MSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhh...eeee.........................................eeeee...eeeeeeeee.......eeeeeeeeee.....eeee.....eee.......eeee....eeeeeeeeeeeeee...eeeeeeee.....eeeeeeeeee.............eeeeeeee.........eeeeeeeeeeee........eeeee.....eeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -FA58C_3  PDB: A:1-152 UniProt: 1-152                                                                                                                    ----------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------FA58C_1  PDB: A:49-78         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wn2 A   0 AMSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249    


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with DIS1A_DICDI | P02886 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:252
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  
          DIS1A_DICDI     2 STQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhh...eeee.........................................eeeee...eeeeeeeee.......eeeeeeeeee.....eeee.....eee.......eeee....eeeeeeeeeeeeee...eeeeeeee.....eeeeeeeeee.............eeeeeeee.........eeeeeeeeeeee........eeeee.....eeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) FA58C_3  PDB: - UniProt: 1-152                                                                                                                         ----------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------FA58C_1  PDB: B:49-78         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wn2 B   2 STQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251  


Chain C from PDB  Type:PROTEIN  Length:253
 aligned with DIS1A_DICDI | P02886 from UniProtKB/Swiss-Prot  Length:253

    Alignment length:253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250   
          DIS1A_DICDI     1 MSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------F5_F8_type_C-2wn2C01 C:16-149                                                                                                         ------------------------------H_lectin-2wn2C04 C:180-252                                               - Pfam domains (1)
           Pfam domains (2) ---------------F5_F8_type_C-2wn2C02 C:16-149                                                                                                         ------------------------------H_lectin-2wn2C05 C:180-252                                               - Pfam domains (2)
           Pfam domains (3) ---------------F5_F8_type_C-2wn2C03 C:16-149                                                                                                         ------------------------------H_lectin-2wn2C06 C:180-252                                               - Pfam domains (3)
         Sec.struct. author ........hhhh...eeee.........................................eeeee...eeeeeeeee.......eeeeeeeeee.....eeee.....eee.......eeee....eeeeeeeeeeeeee...eeeeeeee.....eeeeeeeeee.............eeeeeeee.........eeeeeeeeeeee........eeeee.....eeeeeeee.....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) FA58C_3  PDB: C:1-152 UniProt: 1-152                                                                                                                    ----------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------FA58C_1  PDB: C:49-78         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wn2 C   1 MSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE 253
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
   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  (0, 0)

(no "SCOP Domain" information available for 2WN2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WN2)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: GBD (153)
(-)
Clan: no clan defined [family: H_lectin] (8)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (DIS1A_DICDI | P02886)
molecular function
    GO:0046871    N-acetylgalactosamine binding    Interacting selectively and non-covalently with N-acetylgalactosamine, 2-acetamido-2-deoxygalactopyranose, the n-acetyl derivative of galactosamine.
    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.
    GO:0070492    oligosaccharide binding    Interacting selectively and non-covalently with any oligosaccharide, a molecule with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
biological process
    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:0098609    cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules.
    GO:0007010    cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:0044351    macropinocytosis    An endocytosis process that results in the uptake of liquid material by cells from their external environment by the 'ruffling' of the cell membrane to form heterogeneously sized intracellular vesicles called macropinosomes, which can be up to 5 micrometers in size.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:0009617    response to bacterium    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
    GO:1902168    response to catechin    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a catechin stimulus.
    GO:1904643    response to curcumin    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a curcumin stimulus.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0045335    phagocytic vesicle    A membrane-bounded intracellular vesicle that arises from the ingestion of particulate material by phagocytosis.
    GO:0098636    protein complex involved in cell adhesion    Any protein complex that is capable of carrying out some part of the process of cell adhesion to the cell matrix or to another cell.

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  2wn2
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  DIS1A_DICDI | P02886
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 Related Entries

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

UniProtKB/Swiss-Prot
        DIS1A_DICDI | P02886: 2w94 2w95 2wn3

(-) Related Entries Specified in the PDB File

2w94 NATIVE STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM AT 1.8 ANGSTROM RESOLUTION
2w95 STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH GALNAC AT 1.75 ANGSTROM RESOLUTION
2wn3 CRYSTAL STRUCTURE OF DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH THE DISACCHARIDE GALNAC BETA 1-3 GALACTOSE, AT 1.6 A RESOLUTION.