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Title :   CRYSTAL STRUCTURE OF DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH THE DISACCHARIDE GALNAC BETA 1-3 GALACTOSE, AT 1.6 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 :   1.59

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

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

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 16)

No.	Name	Count	Type	Full Name
1	1PG	1	Ligand/Ion	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2	CA	3	Ligand/Ion	CALCIUM ION
3	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
4	GOL	3	Ligand/Ion	GLYCEROL
5	NGA	3	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:206 , TYR A:241 , GAL A:301 , HOH A:2405 , HOH A:2406 , HOH A:2407 , HOH A:2408 , GLN B:213 , ARG B:215 , TRP B:235 , ASN B:236	BINDING SITE FOR RESIDUE NGA A 300
02	AC2	SOFTWARE	NGA A:300 , ASN B:236	BINDING SITE FOR RESIDUE GAL A 301
03	AC3	SOFTWARE	ASP A:164 , ASP A:203 , ASP A:246 , GLN B:219 , HOH B:2309 , HOH B:2310	BINDING SITE FOR RESIDUE CA A 400
04	AC4	SOFTWARE	SER A:157 , VAL A:158 , THR A:159 , SER B:157 , VAL B:158 , THR B:159 , SER C:157 , VAL C:158 , THR C:159	BINDING SITE FOR RESIDUE SO4 A 401
05	AC5	SOFTWARE	ARG B:104 , VAL B:109 , THR B:110 , HIS B:121 , HOH B:2189	BINDING SITE FOR RESIDUE SO4 A 403
06	AC6	SOFTWARE	ARG A:18 , THR A:57 , TYR A:60 , LYS A:90 , ARG A:92 , TRP A:100 , GLU A:102 , HIS A:135 , HOH A:2223 , HOH A:2409 , ALA C:11	BINDING SITE FOR RESIDUE 1PG A 500
07	AC7	SOFTWARE	ASP B:206 , TYR B:241 , GAL B:301 , HOH B:2363 , HOH B:2364 , HOH B:2365 , HOH B:2367 , GLN C:213 , ARG C:215 , TRP C:235 , ASN C:236	BINDING SITE FOR RESIDUE NGA B 300
08	AC8	SOFTWARE	NGA B:300 , ASN C:236	BINDING SITE FOR RESIDUE GAL B 301
09	AC9	SOFTWARE	ASP B:164 , ASP B:203 , ASP B:246 , GLN C:219 , HOH C:2285 , HOH C:2287	BINDING SITE FOR RESIDUE CA B 400
10	BC1	SOFTWARE	ALA A:0 , MET A:1 , ARG B:92 , HOH B:2368 , HOH B:2369	BINDING SITE FOR RESIDUE SO4 B 402
11	BC2	SOFTWARE	ALA A:11 , ARG B:18 , VAL B:62 , ALA B:133 , HIS B:135	BINDING SITE FOR RESIDUE GOL B 500
12	BC3	SOFTWARE	GLN A:213 , ARG A:215 , TRP A:235 , ASN A:236 , ASP C:206 , GAL C:301 , HOH C:2340 , HOH C:2341 , HOH C:2342	BINDING SITE FOR RESIDUE NGA C 300
13	BC4	SOFTWARE	ASN A:236 , NGA C:300	BINDING SITE FOR RESIDUE GAL C 301
14	BC5	SOFTWARE	GLN A:219 , HOH A:2351 , HOH A:2352 , ASP C:164 , ASP C:203 , ASP C:246	BINDING SITE FOR RESIDUE CA C 400
15	BC6	SOFTWARE	ALA B:11 , ARG C:18 , ARG C:92 , TRP C:100 , HIS C:135	BINDING SITE FOR RESIDUE GOL C 500
16	BC7	SOFTWARE	TYR C:23 , HIS C:27 , THR C:41 , ARG C:79 , GLN C:84 , HIS C:142	BINDING SITE FOR RESIDUE GOL C 501

(no "SS Bond" information available for 2WN3)

(no "Cis Peptide Bond" information available for 2WN3)

(no "SAP(SNP)/Variant" information available for 2WN3)

Asymmetric/Biological Unit (2, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FA58C_3	PS50022	Coagulation factors 5/8 type C domain (FA58C) profile.	DIS1A_DICDI	1-152	2	A:1-152 B:1-152
2	FA58C_1	PS01285	Coagulation factors 5/8 type C domain (FA58C) signature 1.	DIS1A_DICDI	49-78	3	A:49-78 B:49-78 C:49-78

(no "Exon" information available for 2WN3)

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
                 2wn3 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
                 2wn3 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: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 (1) --------------F5_F8_type_C-2wn3C01 C:16-149                                                                                                         ------------------------------H_lectin-2wn3C04 C:180-252                                               - Pfam domains (1)
           Pfam domains (2) --------------F5_F8_type_C-2wn3C02 C:16-149                                                                                                         ------------------------------H_lectin-2wn3C05 C:180-252                                               - Pfam domains (2)
           Pfam domains (3) --------------F5_F8_type_C-2wn3C03 C:16-149                                                                                                         ------------------------------H_lectin-2wn3C06 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: - UniProt: 1-152                                                                                                                         ----------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------------------------FA58C_1  PDB: C:49-78         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wn3 C   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

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 '\|'

(no "SCOP Domain" information available for 2WN3)

(no "CATH Domain" information available for 2WN3)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GBD (153)

Family: F5_F8_type_C (45)

Dictyostelium discoideum (Slime mold) (8)

1a	F5_F8_type_C-2wn3C01	C:16-149
1b	F5_F8_type_C-2wn3C02	C:16-149
1c	F5_F8_type_C-2wn3C03	C:16-149

Clan: no clan defined [family: H_lectin] (8)

Family: H_lectin (8)

Dictyostelium discoideum (Slime mold) (8)

2a	H_lectin-2wn3C04	C:180-252
2b	H_lectin-2wn3C05	C:180-252
2c	H_lectin-2wn3C06	C:180-252

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2wn3)

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	2wn3
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UniProtKB/Swiss-Prot
	DIS1A_DICDI \| P02886	:	2w94 2w95 2wn2

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
2wn2	STRUCTURE OF THE DISCOIDIN I FROM DICTYOSTELIUM DISCOIDEUM IN COMPLEX WITH GALACTOSE BETA 1-3 GALNAC AT 1.8 A RESOLUTION.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 16)

Sites (16, 16)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 5)

Exons (0, 0)

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Pfam Domains (2, 6)

Gene Ontology (16, 16)

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