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(-) Description

Title :  STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH GALNAC AT 1.75 ANGSTROM RESOLUTION
 
Authors :  K. Saboia Aragao, A. Imberty, A. Varrot
Date :  21 Jan 09  (Deposition) - 31 Mar 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Cell Adhesion, H Type 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: PPROEXHTB
    Expression System Strain: ROSETTA2(DE3)PLYSS
    Expression System Taxid: 562
    Organism Common: SLIME MOLD
    Organism Scientific: DICTYOSTELIUM DISCOIDEUM
    Organism Taxid: 366501
    Strain: AX2
    Synonym: DISCOIDIN I, 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  (6, 21)

Asymmetric/Biological Unit (6, 21)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MRD3Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4NGA3Ligand/IonN-ACETYL-D-GALACTOSAMINE
5NI1Ligand/IonNICKEL (II) ION
6SO47Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:213 , ARG A:215 , TRP A:235 , ASN A:236 , HOH A:2366 , HOH A:2367 , ASP C:206BINDING SITE FOR RESIDUE NGA A 254
02AC2SOFTWARETYR A:23 , ARG A:79 , GLN A:84 , HIS A:142 , THR B:41 , HOH B:2085BINDING SITE FOR RESIDUE MPD A 256
03AC3SOFTWAREARG A:104 , VAL A:109 , THR A:110 , HIS A:121 , HOH A:2193 , HOH A:2368BINDING SITE FOR RESIDUE SO4 A 257
04AC4SOFTWAREARG A:92 , TRP A:100 , HOH A:2187 , HOH A:2369 , HOH A:2370 , ASN C:12BINDING SITE FOR RESIDUE MPD A 258
05AC5SOFTWARELYS A:187 , HOH A:2371 , GLY C:178 , LYS C:179 , HOH C:2307BINDING SITE FOR RESIDUE SO4 A 259
06AC6SOFTWAREASP A:164 , ASP A:203 , ASP A:246 , GLN B:219 , HOH B:2293 , HOH B:2295BINDING SITE FOR RESIDUE CA A 260
07AC7SOFTWAREASP A:206 , TYR A:241 , GLN B:213 , ARG B:215 , TRP B:235 , ASN B:236 , HOH B:2342 , HOH B:2344BINDING SITE FOR RESIDUE NGA B 254
08AC8SOFTWARESER A:157 , VAL A:158 , THR A:159 , SER B:157 , VAL B:158 , THR B:159 , HOH B:2242 , SER C:157 , VAL C:158 , THR C:159BINDING SITE FOR RESIDUE SO4 B 255
09AC9SOFTWARETHR A:41 , HOH A:2094 , TYR B:23 , ARG B:79 , GLN B:84 , HIS B:142 , HOH B:2051BINDING SITE FOR RESIDUE MPD B 256
10BC1SOFTWAREARG B:104 , VAL B:109 , THR B:110 , HIS B:121 , HOH B:2345BINDING SITE FOR RESIDUE SO4 B 257
11BC2SOFTWAREHOH B:2346 , GLU C:181 , VAL C:231 , TYR C:233BINDING SITE FOR RESIDUE MRD B 258
12BC3SOFTWAREASP B:114 , ARG B:115 , ASN B:116 , HOH B:2193 , HOH B:2347 , HOH B:2348 , HOH B:2349 , HOH B:2350BINDING SITE FOR RESIDUE SO4 B 259
13BC4SOFTWAREASP B:164 , ASP B:203 , ASP B:246 , GLN C:219 , HOH C:2280 , HOH C:2281BINDING SITE FOR RESIDUE CA B 260
14BC5SOFTWAREHIS A:16 , HIS B:16 , HIS C:16BINDING SITE FOR RESIDUE NI B 261
15BC6SOFTWAREASP B:206 , GLN C:213 , ARG C:215 , TRP C:235 , ASN C:236 , HOH C:2323 , HOH C:2324BINDING SITE FOR RESIDUE NGA C 254
16BC7SOFTWAREGLN B:204 , ARG B:244 , TRP C:235 , HOH C:2325BINDING SITE FOR RESIDUE MRD C 255
17BC8SOFTWARETHR C:41 , ARG C:79 , GLN C:84 , HIS C:142 , HOH C:2041BINDING SITE FOR RESIDUE MPD C 256
18BC9SOFTWAREARG C:104 , VAL C:109 , THR C:110 , HIS C:121 , HOH C:2175 , HOH C:2326 , HOH C:2328BINDING SITE FOR RESIDUE SO4 C 257
19CC1SOFTWAREALA B:11 , ARG C:18 , TYR C:60 , ARG C:92 , HIS C:135 , HOH C:2329BINDING SITE FOR RESIDUE MRD C 258
20CC2SOFTWAREGLY A:168 , ASP A:169 , HOH A:2270 , ARG C:221 , ASN C:222 , HOH C:2330 , HOH C:2331 , HOH C:2332BINDING SITE FOR RESIDUE SO4 C 259
21CC3SOFTWAREGLN A:219 , HOH A:2317 , HOH A:2334 , ASP C:164 , ASP C:203 , ASP C:246BINDING SITE FOR RESIDUE CA C 260

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W95)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W95)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W95)

(-) PROSITE Motifs  (2, 6)

Asymmetric/Biological Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.DIS1A_DICDI1-152
 
 		  3A:1-152
B: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 2W95)

(-) 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
                 2w95 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: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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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: B:1-152 UniProt: 1-152                                                                                                                    ----------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------FA58C_1  PDB: B:49-78         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w95 B   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   


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-2w95C01 C:16-149                                                                                                         ------------------------------H_lectin-2w95C04 C:180-252                                               - Pfam domains (1)
           Pfam domains (2) ---------------F5_F8_type_C-2w95C02 C:16-149                                                                                                         ------------------------------H_lectin-2w95C05 C:180-252                                               - Pfam domains (2)
           Pfam domains (3) ---------------F5_F8_type_C-2w95C03 C:16-149                                                                                                         ------------------------------H_lectin-2w95C06 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
                 2w95 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 2W95)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W95)

(-) 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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  2w95
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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 2wn2 2wn3

(-) Related Entries Specified in the PDB File

2w94 NATIVE STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM AT 1.8 ANGSTROM RESOLUTION