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(-) Description

Title :  CRYSTAL STRUCTURE OF DIOCLEA ROSTRATA LECTIN
 
Authors :  T. M. De Oliveira, P. Delatorre, B. A. M. Da Rocha, E. P. De Sousa, K. S. Nascimento, G. A. Bezerra, T. R. Moura, R. G. Benevides, E. H. S. Bezerra, F. B. M. B. Moreno, V. N. Freire, W. F. De Azevedo Jr. , B. S. Cavada
Date :  22 Oct 07  (Deposition) - 19 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Leguminosae, Lectin, Diocleinae, Dioclea Rostrata, Calcium, Manganese, Metal-Binding, Vacuole, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. De Oliveira, P. Delatorre, B. A. M. Da Rocha, E. P. De Souza, K. S. Nascimento, G. A. Bezerra, T. R. Moura, R. G. Benevides, E. H. S. Bezerra, F. B. M. B. Moreno, V. N. Freire, W. F. De Azevedo Jr. , B. S. Cavada
Crystal Structure Of Dioclea Rostrata Lectin: Insights Into Understanding The Ph-Dependent Dimer-Tetramer Equilibrium And The Structural Basis For Carbohydrate Recognition In Diocleinae Lectins
J. Struct. Biol. V. 164 177 2008
PubMed-ID: 18682294  |  Reference-DOI: 10.1016/J.JSB.2008.05.012
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LECTIN ALPHA CHAIN
    Chains: A
    Organism Scientific: DIOCLEA ROSTRATA
    Organism Taxid: 192416
    Other Details: SEED LECTIN
    Tissue: SEED

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MN1Ligand/IonMANGANESE (II) ION
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MN-1Ligand/IonMANGANESE (II) ION
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:14 , SER A:71 , GLY A:98 , ASP A:208 , GLY A:227 , ARG A:228BINDING SITE FOR RESIDUE PO4 A1285
2AC2SOFTWAREGLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:352 , HOH A:353BINDING SITE FOR RESIDUE MN A 238
3AC3SOFTWAREASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:323 , HOH A:333BINDING SITE FOR RESIDUE CA A 239

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:207 -Asp A:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECA_DIORO5-11  1A:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LECA_DIORO85-94  1A:85-94
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECA_DIORO5-11  4A:5-11
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LECA_DIORO85-94  4A:85-94

(-) Exons   (0, 0)

(no "Exon" information available for 2ZBJ)

(-) Sequences/Alignments

Asymmetric 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:232
 aligned with LECA_DIORO | P58908 from UniProtKB/Swiss-Prot  Length:237

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
           LECA_DIORO     1 ADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYTGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFTFNQFSQNPKDLILQGDATTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDRDPADGITFFIANPDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d2zbja_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2zbjA00 A:1-237  [code=2.60.120.200, no name defined]                                                                                                                                                                                         CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2zbjA01 A:124-237                                                                                      Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------Lectin_legB-2zbjA02 A:124-237                                                                                      Pfam domains (2)
         Sec.struct. author ...eeeeeee...hhhhh.....eeeeee......eeee.......eeeeeeeee....eeeeeeee.....eeeeee.hhhhh...eeeeeeeee........eeeeeeeeeeee.-----.eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeee..........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbj A   1 ADTIVAVELDSYPNTDIGDPNYPHIGIDIKSIRSKSTARWNMQTGKVGTVHISYNSVAKRLSAVVSYTGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKT-----ANSLHFTFNQFSQNPKDLILQGDATTDSDGNLELTKVSSSGDPQGNSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDRDPADGITFFIANPDTSIPSGSGGRLLGLFPDAN 237
                                    10        20        30        40        50        60        70        80        90       100       110      |  -  |    130       140       150       160       170       180       190       200       210       220       230       
                                                                                                                                              117   123
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Concanavalin (293)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (LECA_DIORO | P58908)
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: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:0002553    histamine secretion by mast cell    The regulated release of histamine by a mast cell or group of mast cells.
cellular component
    GO:0033095    aleurone grain    A membrane-bounded storage granule found in cells of the aleurone layer in plants; contains either a protein matrix, protein-carbohydrate bodies and/or globoids. Aleurone grains are formed by the vacuole, rough endoplasmic reticulum and dictyosomes.
    GO:0042629    mast cell granule    Coarse, bluish-black staining cytoplasmic granules, bounded by a plasma membrane and found in mast cells and basophils. Contents include histamine, heparin, chondroitin sulfates, chymase and tryptase.
    GO:0000325    plant-type vacuole    A closed structure that is completely surrounded by a unit membrane, contains liquid, and retains the same shape regardless of cell cycle phase. An example of this structure is found in Arabidopsis thaliana.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

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