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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DIMERIC PROTEIN CORE OF DECORIN, THE ARCHETYPAL SMALL LEUCINE-RICH REPEAT PROTEOGLYCAN
 
Authors :  P. G. Scott, P. A. Mcewan, C. M. Dodd, E. M. Bergmann, P. N. Bishop, J. Bell
Date :  29 Sep 04  (Deposition) - 02 Nov 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Proteoglycan, Leucine-Rich Repeat, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. G. Scott, P. A. Mcewan, C. M. Dodd, E. M. Bergmann, P. N. Bishop, J. Bella
Crystal Structure Of The Dimeric Protein Core Of Decorin, The Archetypal Small Leucine-Rich Repeat Proteoglycan
Proc. Natl. Acad. Sci. Usa V. 101 15633 2004
PubMed-ID: 15501918  |  Reference-DOI: 10.1073/PNAS.0402976101
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DECORIN
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK 293A
    Expression System CommonHUMAN
    Expression System Taxid9606
    Expression System Vector TypeADENOVIRUS
    GeneDCN
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymBONE PROTEOGLYCAN II, PG-S2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:155 , PRO A:156 , LYS A:158 , ASN A:182 , TRP A:308 , HOH A:932 , HOH A:948 , HOH A:949BINDING SITE FOR RESIDUE NAG A 800
2AC2SOFTWAREASN A:233BINDING SITE FOR RESIDUE NAG A 801
3AC3SOFTWAREASN A:274BINDING SITE FOR RESIDUE NAG A 802

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:25 -A:31
2A:29 -A:38
3A:284 -A:317

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XKU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XKU)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.PGS2_BOVIN83-104
107-128
131-152
153-173
223-243
247-268
271-293
294-315
  8A:53-74
A:77-98
A:101-122
A:123-143
A:193-213
A:217-238
A:241-263
A:264-285
Biological Unit 1 (1, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LRRPS51450 Leucine-rich repeat profile.PGS2_BOVIN83-104
107-128
131-152
153-173
223-243
247-268
271-293
294-315
  16A:53-74
A:77-98
A:101-122
A:123-143
A:193-213
A:217-238
A:241-263
A:264-285

(-) Exons   (7, 7)

Asymmetric Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSBTAT000000045621ENSBTAE00000300120chr5:23762660-23762470191PGS2_BOVIN-00--
1.3ENSBTAT000000045623ENSBTAE00000036594chr5:23758480-23758234247PGS2_BOVIN1-72721A:22-4221
1.4ENSBTAT000000045624ENSBTAE00000036606chr5:23746370-23746258113PGS2_BOVIN72-109381A:42-7938
1.5ENSBTAT000000045625ENSBTAE00000036610chr5:23739602-23739389214PGS2_BOVIN110-181721A:80-15172
1.6ENSBTAT000000045626ENSBTAE00000036614chr5:23738587-23738474114PGS2_BOVIN181-219391A:151-18939
1.7ENSBTAT000000045627ENSBTAE00000036619chr5:23732791-2373269894PGS2_BOVIN219-250321A:189-22032
1.8ENSBTAT000000045628ENSBTAE00000036625chr5:23728847-23728709139PGS2_BOVIN250-296471A:220-26647
1.9bENSBTAT000000045629bENSBTAE00000036725chr5:23724466-237234381029PGS2_BOVIN297-360641A:267-32660

(-) 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:305
 aligned with PGS2_BOVIN | P21793 from UniProtKB/Swiss-Prot  Length:360

    Alignment length:305
                                    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     
           PGS2_BOVIN    52 GPVCPFRCQCHLRVVQCSDLGLEKVPKDLPPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQL 356
               SCOP domains d1xkua_ A: Decorin                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1xkuA00 A:22-326 Ribonuclease Inhibitor                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eee..................eee.....................eee.....................eee..................eee.........hhhhhh......eee......hhhhh..hhhhhh....eee..................eee.......ee.hhhhh......eee.......ee...hhhhh....eee....................eee...........................eee......hhhhhhhhhhh...hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------LRR  PDB: A:53-74     --LRR  PDB: A:77-98     --LRR  PDB: A:101-122   LRR  PDB: A:123-143  -------------------------------------------------LRR  PDB: A:193-213  ---LRR  PDB: A:217-238   --LRR  PDB: A:241-263    LRR  PDB: A:264-285   ----------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:22-4-------------------------------------Exon 1.5  PDB: A:80-151 UniProt: 110-181                                -------------------------------------Exon 1.7  PDB: A:189-220        ----------------------------------------------Exon 1.9b  PDB: A:267-326 UniProt: 297-360 [INCOMPLETE]      Transcript 1 (1)
           Transcript 1 (2) --------------------Exon 1.4  PDB: A:42-79 UniProt: 72-109-----------------------------------------------------------------------Exon 1.6  PDB: A:151-189               ------------------------------Exon 1.8  PDB: A:220-266 UniProt: 250-296      ------------------------------------------------------------ Transcript 1 (2)
                 1xku A  22 GPVCPFRCQCHLRVVQCSDLGLEKVPKDLPPDTALLDLQNNKITEIKDGDFKNLKNLHTLILINNKISKISPGAFAPLVKLERLYLSKNQLKELPEKMPKTLQELRVHENEITKVRKSVFNGLNQMIVVELGTNPLKSSGIENGAFQGMKKLSYIRIADTNITTIPQGLPPSLTELHLDGNKITKVDAASLKGLNNLAKLGLSFNSISAVDNGSLANTPHLRELHLNNNKLVKVPGGLADHKYIQVVYLHNNNISAIGSNDFCPPGYNTKKASYSGVSLFSNPVQYWEIQPSTFRCVYVRAAVQL 326
                                    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     

   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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XKU)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (PGS2_BOVIN | P21793)
molecular function
    GO:0005518    collagen binding    Interacting selectively and non-covalently with collagen, a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals. Collagen is highly enriched in glycine (some regions are 33% glycine) and proline, occurring predominantly as 3-hydroxyproline (about 20%).
    GO:0050840    extracellular matrix binding    Interacting selectively and non-covalently with a component of the extracellular matrix.
    GO:0005539    glycosaminoglycan binding    Interacting selectively and non-covalently with any glycan (polysaccharide) containing a substantial proportion of aminomonosaccharide residues.
    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:0004860    protein kinase inhibitor activity    Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
biological process
    GO:0019221    cytokine-mediated signaling pathway    A series of molecular signals initiated by the binding of a cytokine to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0046426    negative regulation of JAK-STAT cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of the JAK-STAT signaling pathway activity.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0019800    peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan    The formation of a cross-link between peptide chains mediated by a chondroitin 4-sulfate glycosaminoglycan that originates from a typical O-glycosidic link to serine of one chain; the other chain is esterified, via the alpha-carbon of its C-terminal Asp, to C-6 of an internal N-acetylgalactosamine of the glycosaminoglycan chain.
    GO:0010508    positive regulation of autophagy    Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PGS2_BOVIN | P217931xcd 1xec

(-) Related Entries Specified in the PDB File

1xcd DIMERIC BOVINE TISSUE-EXTRACTED DECORIN, CRYSTAL FORM 1
1xec DIMERIC BOVINE TISSUE-EXTRACTED DECORIN, CRYSTAL FORM 2