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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE GALECTIN-9 N-TERMINAL CRD IN COMPLEX WITH N-ACETYLLACTOSAMINE
 
Authors :  M. Nagae, N. Nishi, T. Nakamura, T. Murata, S. Wakatsuki, R. Kato
Date :  14 Nov 05  (Deposition) - 26 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Sandwich, Carbohydrate Binding Protein, Galectin, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nagae, N. Nishi, T. Murata, T. Usui, T. Nakamura, S. Wakatsuki, R. Kato
Crystal Structure Of The Galectin-9 N-Terminal Carbohydrate Recognition Domain From Mus Musculus Reveals The Basic Mechanism Of Carbohydrate Recognition
J. Biol. Chem. V. 281 35884 2006
PubMed-ID: 16990264  |  Reference-DOI: 10.1074/JBC.M606648200

(-) Compounds

Molecule 1 - LECTIN, GALACTOSE BINDING, SOLUBLE 9
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX4T-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN(RESIDUES 1-157)
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GALECTIN-9

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:60 , ASN A:62 , ARG A:64 , ASN A:74 , TRP A:81 , GLU A:84 , NAG A:501 , HOH A:538 , HOH A:550 , HOH A:567 , HOH A:620BINDING SITE FOR RESIDUE GAL A 500
2AC2SOFTWAREARG A:64 , GLU A:84 , ARG A:86 , GAL A:500 , HOH A:567 , HOH A:623BINDING SITE FOR RESIDUE NAG A 501
3AC3SOFTWAREHIS B:60 , ASN B:62 , ARG B:64 , ASN B:74 , TRP B:81 , GLU B:84 , NAG B:601 , HOH B:611 , HOH B:644 , HOH B:668BINDING SITE FOR RESIDUE GAL B 600
4AC4SOFTWAREHOH A:600 , ARG B:64 , GLU B:84 , ARG B:86 , GAL B:600 , HOH B:643 , HOH B:666 , HOH B:670BINDING SITE FOR RESIDUE NAG B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D6N)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:15 -Pro A:16
2Ile B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D6N)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GALECTINPS51304 Galactoside-binding lectin (galectin) domain profile.LEG9_MOUSE17-147
 
225-353		  2A:17-147
B:17-147
-

(-) Exons   (0, 0)

(no "Exon" information available for 2D6N)

(-) 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:152
 aligned with LEG9_MOUSE | O08573 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:183
                              1                                                                                                                                                                                    
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178   
           LEG9_MOUSE     - --MALFSAQSPYINPIIPFTGPIQGGLQEGLQVTLQGTTKSFAQRFVVNFQNSFNGNDIAFHFNPRFEEGGYVVCNTKQNGQWGPEERKMQMPFQKGMPFELCFLVQRSEFKVMVNKKFFVQYQHRVPYHLVDTIAVSGCLKLSFITFQNSAAPVQHVFSTLQFSQPVQFPRTPKGRKQKTQN 181
               SCOP domains d2d6na_ A: automated matches                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee.....eeee.........eeeeeeee......eeeeee.......eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeee-------------------------------e.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------GALECTIN  PDB: A:17-147 UniProt: 17-147                                                                                            ---------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d6n A  -1 GSMALFSAQSPYINPIIPFTGPIQGGLQEGLQVTLQGTTKSFAQRFVVNFQNSFNGNDIAFHFNPRFEEGGYVVCNTKQNGQWGPEERKMQMPFQKGMPFELCFLVQRSEFKVMVNKKFFVQYQHRVPYHLVDTIAVSGCLKLSFITFQ-------------------------------TQN 150
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138        |-         -         -         -|  
                                                                                                                                                                              147                             148  


Chain B from PDB  Type:PROTEIN  Length:153
 aligned with LEG9_MOUSE | O08573 from UniProtKB/Swiss-Prot  Length:353

    Alignment length:184
                              1                                                                                                                                                                                     
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178    
           LEG9_MOUSE     - --MALFSAQSPYINPIIPFTGPIQGGLQEGLQVTLQGTTKSFAQRFVVNFQNSFNGNDIAFHFNPRFEEGGYVVCNTKQNGQWGPEERKMQMPFQKGMPFELCFLVQRSEFKVMVNKKFFVQYQHRVPYHLVDTIAVSGCLKLSFITFQNSAAPVQHVFSTLQFSQPVQFPRTPKGRKQKTQNF 182
               SCOP domains d2d6nb_ B: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee....ee.....eeee........eeeeeeeee......eeeeee.......eeeeeeee.....eeeeeeee..ee...eee.........eeeeeeee...eeeeee..eeeeeee...hhhhh.eeeeee.eeeeeeeee-------------------------------e... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------GALECTIN  PDB: B:17-147 UniProt: 17-147                                                                                            ----------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d6n B  -1 GSMALFSAQSPYINPIIPFTGPIQGGLQEGLQVTLQGTTKSFAQRFVVNFQNSFNGNDIAFHFNPRFEEGGYVVCNTKQNGQWGPEERKMQMPFQKGMPFELCFLVQRSEFKVMVNKKFFVQYQHRVPYHLVDTIAVSGCLKLSFITFQ-------------------------------TQNF 151
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138        |-         -         -         -|   
                                                                                                                                                                              147                             148
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D6N)

(-) Gene Ontology  (44, 44)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (LEG9_MOUSE | O08573)
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:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0016936    galactoside binding    Interacting selectively and non-covalently with any glycoside in which the sugar group is galactose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043539    protein serine/threonine kinase activator activity    Binds to and increases the activity of a protein serine/threonine kinase.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
    GO:0098586    cellular response to virus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0007565    female pregnancy    The set of physiological processes that allow an embryo or foetus to develop within the body of a female animal. It covers the time from fertilization of a female ovum by a male spermatozoon until birth.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045185    maintenance of protein location    Any process in which a protein is maintained in a location and prevented from moving elsewhere. These include sequestration, stabilization to prevent transport elsewhere and the active retrieval of proteins that do move away.
    GO:2000562    negative regulation of CD4-positive, alpha-beta T cell proliferation    Any process that stops, prevents or reduces the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0032689    negative regulation of interferon-gamma production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:1902714    negative regulation of interferon-gamma secretion    Any process that stops, prevents or reduces the frequency, rate or extent of interferon-gamma secretion.
    GO:0032815    negative regulation of natural killer cell activation    Any process that stops, prevents, or reduces the frequency, rate or extent of natural killer cell activation.
    GO:0043322    negative regulation of natural killer cell degranulation    Any process that stops, prevents, or reduces the rate of natural killer cell degranulation.
    GO:2000406    positive regulation of T cell migration    Any process that activates or increases the frequency, rate or extent of T cell migration.
    GO:0032722    positive regulation of chemokine production    Any process that activates or increases the frequency, rate, or extent of chemokine production.
    GO:0001819    positive regulation of cytokine production    Any process that activates or increases the frequency, rate or extent of production of a cytokine.
    GO:1900426    positive regulation of defense response to bacterium    Any process that activates or increases the frequency, rate or extent of defense response to bacterium.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045089    positive regulation of innate immune response    Any process that activates or increases the frequency, rate or extent of the innate immune response, the organism's first line of defense against infection.
    GO:0032732    positive regulation of interleukin-1 production    Any process that activates or increases the frequency, rate, or extent of interleukin-1 production.
    GO:2001181    positive regulation of interleukin-10 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-10 secretion.
    GO:2000778    positive regulation of interleukin-6 secretion    Any process that activates or increases the frequency, rate or extent of interleukin-6 secretion.
    GO:0043032    positive regulation of macrophage activation    Any process that stimulates, induces or increases the rate of macrophage activation.
    GO:0051353    positive regulation of oxidoreductase activity    Any process that activates or increases the frequency, rate or extent of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered.
    GO:0010862    positive regulation of pathway-restricted SMAD protein phosphorylation    Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0071902    positive regulation of protein serine/threonine kinase activity    Any process that increases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0045591    positive regulation of regulatory T cell differentiation    Any process that activates or increases the frequency, rate or extent of differentiation of regulatory T cells.
    GO:2000679    positive regulation of transcription regulatory region DNA binding    Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding.
    GO:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    GO:0010819    regulation of T cell chemotaxis    Any process that modulates the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus.
    GO:0033081    regulation of T cell differentiation in thymus    Any process that modulates the frequency, rate or extent of T cell differentiation in the thymus.
    GO:2000316    regulation of T-helper 17 type immune response    Any process that modulates the frequency, rate or extent of T-helper 17 type immune response.
    GO:0032823    regulation of natural killer cell differentiation    Any process that modulates the frequency, rate or extent of natural killer cell differentiation.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LEG9_MOUSE | O08573: 2d6k 2d6l 2d6m 2d6o 2d6p

(-) Related Entries Specified in the PDB File

2d6k THE SAME PROTEIN(CRYSTAL FORM1)
2d6l THE SAME PROTEIN(CRYSTAL FORM2)
2d6m THE SAME PROTEIN(LACTOSE COMPLEX)
2d6o THE SAME PROTEIN(LN2 COMPLEX)
2d6p THE SAME PROTEIN(T-ANTIGEN COMPLEX)