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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN GOAT SIGNALLING PROTEIN AND THE HEXASACCHARIDE AT 2.28 A RESOLUTION
 
Authors :  J. Kumar, A. S. Ethayathulla, D. B. Srivastava, N. Singh, S. Sharma, T. P
Date :  09 Jul 06  (Deposition) - 01 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym./Biol. Unit :  A
Keywords :  Tim Barrel, Signalling, Involution, Mammary Gland, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Kumar, A. S. Ethayathulla, D. B. Srivastava, N. Singh, S. Sharma, P. Kaur, A. Srinivasan, T. P. Singh
Carbohydrate-Binding Properties Of Goat Secretory Glycoprotein (Spg-40) And Its Functional Implications: Structures Of The Native Glycoprotein And Its Four Complexe With Chitin-Like Oligosaccharides
Acta Crystallogr. , Sect. D V. 63 437 2007
PubMed-ID: 17372347  |  Reference-DOI: 10.1107/S0907444907001631

(-) Compounds

Molecule 1 - CHITINASE-3-LIKE PROTEIN 1
    ChainsA
    Organism CommonGOAT
    Organism ScientificCAPRA HIRCUS
    Organism Taxid9925
    SecretionMILK MAMMARY GLAND
    SynonymSPG-40, MAMMARY GLAND PROTEIN MGP-40, BP40

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1MAN3Ligand/IonALPHA-D-MANNOSE
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:39 , ILE A:40 , SER A:41 , ARG A:84 , NAG A:364 , HOH A:436BINDING SITE FOR RESIDUE NAG A 363
02AC2SOFTWARENAG A:363 , MAN A:365BINDING SITE FOR RESIDUE NAG A 364
03AC3SOFTWARENAG A:364 , MAN A:366BINDING SITE FOR RESIDUE MAN A 365
04AC4SOFTWAREMAN A:365 , MAN A:367BINDING SITE FOR RESIDUE MAN A 366
05AC5SOFTWAREMAN A:366BINDING SITE FOR RESIDUE MAN A 367
06AC6SOFTWARETRP A:78 , TYR A:120 , LEU A:183 , ASP A:186 , NAG A:369BINDING SITE FOR RESIDUE NAG A 368
07AC7SOFTWAREPHE A:37 , TRP A:78 , LEU A:183 , TYR A:185 , ASP A:186 , PHE A:240 , ARG A:242 , TRP A:331 , NAG A:368 , NAG A:370BINDING SITE FOR RESIDUE NAG A 369
08AC8SOFTWARETRP A:10 , PHE A:37 , GLY A:77 , TRP A:78 , ASN A:79 , GLU A:269 , TRP A:331 , NAG A:369 , NAG A:371 , HOH A:395BINDING SITE FOR RESIDUE NAG A 370
09AC9SOFTWARETRP A:48 , ASN A:79 , GLU A:269 , NAG A:370 , NAG A:372 , HOH A:395BINDING SITE FOR RESIDUE NAG A 371
10BC1SOFTWARETYR A:13 , GLU A:49 , NAG A:371 , NAG A:373BINDING SITE FOR RESIDUE NAG A 372
11BC2SOFTWARETYR A:13 , GLU A:49 , TRP A:50 , NAG A:372BINDING SITE FOR RESIDUE NAG A 373

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:30
2A:279 -A:343

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:36 -Phe A:37
2Leu A:119 -Tyr A:120
3Trp A:331 -Ala A:332

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DT3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DT3)

(-) Exons   (0, 0)

(no "Exon" information available for 2DT3)

(-) 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:361
 aligned with CH3L1_CAPHI | Q8SPQ0 from UniProtKB/Swiss-Prot  Length:383

    Alignment length:362
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381  
          CH3L1_CAPHI    22 YKLICYYTSWSQYREGDGSCFPDAIDPFLCTHIIYSFANISNNEIDTWEWNDVTLYDTLNTLKNRNPKLKTLLSVGGWNFGPERFSKIASKTQSRRTFIKSVPPFLRTHGFDGLDLAWLYPGRRDKRHLTGLVKEMKAEFAREAQAGTERLLLSAAVSAGKIAIDRGYDIAQISRHLDFISLLTYDFHGAWRQTVGHHSPLFRGQEDASSDRFSNADYAVSYMLRLGAPANKLVMGIPTFGRSFTLASSKTDVGAPISGPGIPGRFTKEKGILAYYEICDFLHGATTHRFRDQQVPYATKGNQWVAYDDQESVKNKARYLKNRQLAGAMVWALDLDDFRGTFCGQNLTFPLTSAVKDVLAEV 383
               SCOP domains d2dt3a1 A:1-239,A:308-362 Signal processing protein (SPC-40, MGP-40)                                                                                                                                                                           d2dt3a2 A:240-307 Signal processing protein (SPC-40, MGP-40)        d2dt3a1 A:1-239,A:308-362                               SCOP domains
               CATH domains 2dt3A01 A:1-239,A:308-362 Glycosidases                                                                                                                                                                                                         2dt3A02 A:240-307  [code=3.10.50.10, no name defined]               2dt3A01 A:1-239,A:308-362 Glycosidases                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhh.hhhhh......eeeeeeeeee..eee....hhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhh....eeee............................-...hhhhhhhhhhhhh.hhh.eeeeee.eeeeeee..........eeee...........eeehhhhhhhh...eeeee....eeeeee..eeee..hhhhhhhhhhhhhhh...eeeeehhhhh............hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dt3 A   1 YKLICYYTSWSQYREGDGSCFPDAIDPFLCTHVIYSFANISNNEIDTWEWNDVTLYDTLNTLKNRNPKLKTLLSVGGWNFGPERFSKIASKTQSRRTFIKSVPPFLRTHGFDGLDLAWLYPGRRDKRHLTALVKEMKAEFAREAQAGTERLLLSAAVSAGKIAIDRGYDIAQISRHLDFISLLTYDFHGAWRQTVGHHSPLFRGNSDASS-RFSNADYAVSYMLRLGAPANKLVMGIPTFGRSFTLASSKTDVGAPISGPGIPGRFTKEKGILAYYEICDFLHGATTHRFRDQQVPYATKGNQWVAYDDQESVKNKARYLKNRQLAGAMVWALDLDDFRGTFCGQNLTFPLTSAVKDVLARV 362
                                    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       260       270       280       290       300       310       320       330       340       350       360  
                                                                                                                                                                                                                                           210 |                                                                                                                                                      
                                                                                                                                                                                                                                             212                                                                                                                                                      

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DT3)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CH3L1_CAPHI | Q8SPQ0)
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:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
biological process
    GO:0007250    activation of NF-kappaB-inducing kinase activity    The stimulation of the activity of NF-kappaB-inducing kinase through phosphorylation at specific residues.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0071356    cellular response to tumor necrosis factor    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 tumor necrosis factor stimulus.
    GO:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0072606    interleukin-8 secretion    The regulated release of interleukin-8 from a cell.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0045766    positive regulation of angiogenesis    Any process that activates or increases angiogenesis.
    GO:0010800    positive regulation of peptidyl-threonine phosphorylation    Any process that increases the frequency, rate or extent of peptidyl-threonine phosphorylation. Peptidyl-threonine phosphorylation is the phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0051897    positive regulation of protein kinase B signaling    Any process that activates or increases the frequency, rate or extent of protein kinase B signaling, a series of reactions mediated by the intracellular serine/threonine kinase protein kinase B.
    GO:0070555    response to interleukin-1    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 an interleukin-1 stimulus.
    GO:0070741    response to interleukin-6    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 an interleukin-6 stimulus.
    GO:0009612    response to mechanical stimulus    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 mechanical stimulus.
    GO:0034612    response to tumor necrosis factor    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 tumor necrosis factor stimulus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CH3L1_CAPHI | Q8SPQ01ljy 1syt 1zbv 1zbw 1zu8 2aos 2b31 2dsz 2dt0 2dt1 2dt2 2o92 2olh

(-) Related Entries Specified in the PDB File

2dpe 2dsz 2dt0 2dt1 2dt2 2esc