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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN MUTANT E123A-H131N-K132Q COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE
 
Authors :  C. S. Nagano, L. Sanz, B. S. Cavada, J. J. Calvete
Date :  16 Jan 07  (Deposition) - 30 Oct 07  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cona-Like, Metal-Binding, Legume Lectin, Carbohydrate Binding Protein, Sugar-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Nagano, J. J. Calvete, D. Barettino, A. Perez, B. S. Cavada, L. San
Insights Into The Structural Basis Of The Ph- Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis Of Recombinant Diocleinae Lectins.
Biochem. J. V. 409 417 2008
PubMed-ID: 17937659  |  Reference-DOI: 10.1042/BJ20070942

(-) Compounds

Molecule 1 - LECTIN ALPHA CHAIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: DIOCLEA GRANDIFLORA
    Organism Taxid: 3837

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MN8Ligand/IonMANGANESE (II) ION
3XMM4Ligand/Ion(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:12 , TYR A:14 , ASN A:16 , ASP A:21 , HOH A:2189 , HOH A:2207BINDING SITE FOR RESIDUE CA A 240
02AC2SOFTWAREGLU A:10 , ASP A:12 , ASP A:21 , HIS A:26 , HOH A:2216 , HOH A:2217BINDING SITE FOR RESIDUE MN A 241
03AC3SOFTWAREHIS A:53 , ASP A:194 , HOH A:2172 , HOH A:2221 , HOH A:2222 , HOH A:2223BINDING SITE FOR RESIDUE MN A 243
04AC4SOFTWARETYR A:14 , ASN A:16 , GLY A:100 , LEU A:101 , TYR A:102 , ALA A:209 , ASP A:210 , GLY A:229 , ARG A:230 , HOH A:2112 , HOH A:2218 , HOH A:2219 , HOH A:2220 , ILE B:31 , ASN B:85BINDING SITE FOR RESIDUE XMM A 242
05AC5SOFTWAREASP B:12 , TYR B:14 , ASN B:16 , ASP B:21 , HOH B:2150 , HOH B:2162BINDING SITE FOR RESIDUE CA B 240
06AC6SOFTWAREGLU B:10 , ASP B:12 , ASP B:21 , HIS B:26 , HOH B:2171 , HOH B:2172BINDING SITE FOR RESIDUE MN B 241
07AC7SOFTWAREHIS B:53 , HOH B:2176BINDING SITE FOR RESIDUE MN B 243
08AC8SOFTWARETYR B:14 , ASN B:16 , GLY B:100 , LEU B:101 , TYR B:102 , ALA B:209 , ASP B:210 , GLY B:229 , ARG B:230 , HOH B:2173 , HOH B:2174 , HOH B:2175BINDING SITE FOR RESIDUE XMM B 242
09AC9SOFTWAREASP C:12 , TYR C:14 , ASN C:16 , ASP C:21 , HOH C:2134 , HOH C:2149BINDING SITE FOR RESIDUE CA C 240
10BC1SOFTWAREGLU C:10 , ASP C:12 , ASP C:21 , HIS C:26 , HOH C:2158 , HOH C:2159BINDING SITE FOR RESIDUE MN C 241
11BC2SOFTWARELYS B:118 , SER B:192 , HIS C:53 , ASP C:194 , HOH C:2125 , HOH C:2162BINDING SITE FOR RESIDUE MN C 243
12BC3SOFTWAREASN A:239 , ASN C:16 , GLY C:100 , LEU C:101 , TYR C:102 , ALA C:209 , ASP C:210 , GLY C:229 , ARG C:230 , HOH C:2117 , HOH C:2160 , HOH C:2161BINDING SITE FOR RESIDUE XMM C 242
13BC4SOFTWAREASP D:12 , TYR D:14 , ASN D:16 , ASP D:21 , HOH D:2009 , HOH D:2164BINDING SITE FOR RESIDUE CA D 240
14BC5SOFTWAREGLU D:10 , ASP D:12 , ASP D:21 , HIS D:26 , HOH D:2175 , HOH D:2176BINDING SITE FOR RESIDUE MN D 241
15BC6SOFTWAREHOH A:2171 , HIS D:53 , ASP D:194 , HOH D:2179BINDING SITE FOR RESIDUE MN D 243
16BC7SOFTWAREARG A:35 , ASN A:239 , ASN D:16 , GLY D:100 , LEU D:101 , TYR D:102 , ALA D:209 , ASP D:210 , GLY D:229 , ARG D:230 , HOH D:2130 , HOH D:2177 , HOH D:2178BINDING SITE FOR RESIDUE XMM D 242

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:209 -Asp A:210
2Ala B:209 -Asp B:210
3Ala C:209 -Asp C:210
4Ala D:209 -Asp D:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECA_DIOGR5-11
 
 
 		  4A:7-13
B:7-13
C:7-13
D:7-13
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LECA_DIOGR85-94
 
 
 		  4A:87-96
B:87-96
C:87-96
D:87-96

(-) Exons   (0, 0)

(no "Exon" information available for 2JEC)

(-) 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:238
 aligned with LECA_DIOGR | P08902 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:238
                             1                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229        
           LECA_DIOGR     - -ADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADENSLHFSFHKFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d2jeca_ A: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2jecA00 A:2-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee.....eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee......eeeeeeee........eeeee..ee.....ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jec A   2 MADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFNQFSQNPKDLILQGDAFTDSDGNLQLTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain B from PDB  Type:PROTEIN  Length:238
 aligned with LECA_DIOGR | P08902 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:238
                             1                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229        
           LECA_DIOGR     - -ADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADENSLHFSFHKFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d2jecb_ B: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2jecB00 B:2-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee.....eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.......eeeeeeee........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jec B   2 MADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFNQFSQNPKDLILQGDAFTDSDGNLQLTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain C from PDB  Type:PROTEIN  Length:238
 aligned with LECA_DIOGR | P08902 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:238
                             1                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229        
           LECA_DIOGR     - -ADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADENSLHFSFHKFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d2jecc_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2jecC00 C:2-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee..eeeeeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee......................eeeee..ee.....ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jec C   2 MADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFNQFSQNPKDLILQGDAFTDSDGNLQLTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231        


Chain D from PDB  Type:PROTEIN  Length:238
 aligned with LECA_DIOGR | P08902 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:238
                             1                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229        
           LECA_DIOGR     - -ADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADENSLHFSFHKFSQNPKDLILQGDAFTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWESSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d2jecd_ D: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2jecD00 D:2-239  [code=2.60.120.200, no name defined]                                                                                                                                                                                          CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2jecD01 D:126-239                                                                                      Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2jecD02 D:126-239                                                                                      Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2jecD03 D:126-239                                                                                      Pfam domains (3)
           Pfam domains (4) ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2jecD04 D:126-239                                                                                      Pfam domains (4)
           Pfam domains (5) ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2jecD05 D:126-239                                                                                      Pfam domains (5)
           Pfam domains (6) ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2jecD06 D:126-239                                                                                      Pfam domains (6)
           Pfam domains (7) ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2jecD07 D:126-239                                                                                      Pfam domains (7)
           Pfam domains (8) ----------------------------------------------------------------------------------------------------------------------------Lectin_legB-2jecD08 D:126-239                                                                                      Pfam domains (8)
         Sec.struct. author ....eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee.....eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeeee......................eeeee..ee.....ee..............eeeeee...ee.....eeeeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jec D   2 MADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYSGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFNQFSQNPKDLILQGDAFTDSDGNLQLTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDREPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 239
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
   Legend:   → Mismatch (orange background)
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  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, 8)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (LECA_DIOGR | P08902)
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.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0008150    biological_process    Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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    Ala A:209 - Asp A:210   [ RasMol ]  
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    Ala D:209 - Asp D:210   [ RasMol ]  
 

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  LECA_DIOGR | P08902
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 Related Entries

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

UniProtKB/Swiss-Prot
        LECA_DIOGR | P08902: 1dgl 1vln 2gdf 2je9 4z8b

(-) Related Entries Specified in the PDB File

1dgl LECTIN FROM DIOCLEA GRANDIFLORA COMPLEXED TO TRIMANNOSIDE
1vln A TRICLINIC CRYSTAL FORM OF THE LECTIN CONCANAVALIN A
2jdz CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GUIANENSIS LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE
2je7 CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GUIANENSIS LECTIN S131H COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A -D-MANNOSE
2je9 CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN COMPLEXED WITH 5-BROMO-4 -CHLORO-3-INDOLYL-A-D-MANNOSE