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(-) Description

Title :  CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GUIANENSIS LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE
 
Authors :  C. S. Nagano, L. Sanz, B. S. Cavada, J. J. Calvete
Date :  12 Jan 07  (Deposition) - 30 Oct 07  (Release) - 29 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Carbohydrate-Binding Protein, Metal-Binding, Legume Lectin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Nagano, J. J. Calvete, D. Barettino, A. Perez, B. S. Cavada, L. Sanz
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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: RDGUIA/PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET32A
    Organism Scientific: DIOCLEA GUIANENSIS
    Organism Taxid: 99571
    Synonym: RDGUIA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2CD1Ligand/IonCADMIUM ION
3MN5Ligand/IonMANGANESE (II) ION
4XMM1Ligand/Ion(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CD-1Ligand/IonCADMIUM ION
3MN-1Ligand/IonMANGANESE (II) ION
4XMM4Ligand/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  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:10 , ASP A:12 , ASP A:21 , HIS A:26 , HOH A:2068 , HOH A:2069BINDING SITE FOR RESIDUE MN A 240
2AC2SOFTWAREASP A:12 , TYR A:14 , ASN A:16 , ASP A:21 , HOH A:2003 , HOH A:2057BINDING SITE FOR RESIDUE CA A 241
3AC3SOFTWARESER A:136 , HIS A:182 , HOH A:2070 , HOH A:2071 , HOH A:2072BINDING SITE FOR RESIDUE MN A 244
4AC4SOFTWAREGLU A:89 , GLU A:185 , HOH A:2031BINDING SITE FOR RESIDUE CD A 245
5AC5SOFTWARESER A:127 , HIS A:129 , HOH A:2073 , HOH A:2074 , HOH A:2075BINDING SITE FOR RESIDUE MN A 246
6AC6SOFTWAREASP A:207 , HOH A:2076BINDING SITE FOR RESIDUE MN A 247
7AC7SOFTWAREHIS A:53 , ASP A:194 , HOH A:2077 , HOH A:2078 , HOH A:2079BINDING SITE FOR RESIDUE MN A 248
8AC8SOFTWARETYR 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:2080BINDING SITE FOR RESIDUE XMM A 249

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:123 -Asp A:124
2Ala A:209 -Asp A:210

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECA_DIOGU5-11  1A:7-13
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LECA_DIOGU85-94  1A:87-96
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LECTIN_LEGUME_BETAPS00307 Legume lectins beta-chain signature.LECA_DIOGU5-11  4A:7-13
2LECTIN_LEGUME_ALPHAPS00308 Legume lectins alpha-chain signature.LECA_DIOGU85-94  4A:87-96

(-) Exons   (0, 0)

(no "Exon" information available for 2JDZ)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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   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:235
 aligned with LECA_DIOGU | P81637 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_DIOGU     1 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLSAVVSYTGSSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTNSIADANSLHFSFNQFSQNPKDLILQSDATTDSDGNLELTKVSSSGDPQGSSVGRALFYAPVHIWEKSAVVAGFDATFTFLIKSPDRDPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 237
               SCOP domains d2jdza_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2jdzA00 A:3-239  [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..--...eeeeeee.........eeeee..ee.....ee..............eeeeee...ee.......eeeeeeeeeee..........eeeeeeee.........hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----LECTIN_-------------------------------------------------------------------------LECTIN_LEG----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jdz A   3 ADTIVAVELDSYPNTDIGDPSYPHIGIDIKSIRSKSTARWNMQTGKVGTAHISYNSVAKRLSAVVSYSGTSSTTVSYDVDLNNVLPEWVRVGLSATTGLYKETNTILSWSFTSKLKTN--ADANSLHFSFSQFSQNPKDLILQSDATTDSDGNLQLTRVSSDGSPQGSSVGRALFYAPVHIWEKSAVVASFDATFTFLIKSPDRDPADGITFFIANTDTSIPSGSGGRLLGLFPDAN 239
                                    12        22        32        42        52        62        72        82        92       102       112       | -|      132       142       152       162       172       182       192       202       212       222       232       
                                                                                                                                               120  |                                                                                                                    
                                                                                                                                                  123
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2JDZ)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (LECA_DIOGU | P81637)
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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        LECA_DIOGU | P81637: 1h9p 1h9w 2je7

(-) Related Entries Specified in the PDB File

1h9p CRYSTAL STRUCTURE OF DIOCLEA GUIANENSIS SEED LECTIN
1h9w NATIVE DIOCLEA GUIANENSIS SEED LECTIN
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
2jec CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN MUTANT E123A-H131N-K132Q COMPLEXED WITH 5-BROMO -4-CHLORO-3-INDOLYL-A-D-MANNOSE