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(-) Description

Title :  SOLUTION STRUCTURE OF AN EGF PAIR (EGF34) FROM VITAMIN K-DEPENDENT PROTEIN S
 
Authors :  T. Drakenberg, H. Ghasriani, E. Thulin, A. M. Thamlitz, A. Muranyi, A. Annila, J. Stenflo
Date :  22 Mar 05  (Deposition) - 21 Jun 05  (Release) - 28 Apr 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Egf Module, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Drakenberg, H. Ghasriani, E. Thulin, A. Muranyi, A. Annila, J. Stenflo
Solution Structure Of The Ca(2+)-Binding Egf3-4 Pair From Vitamin K-Dependent Protein S: Identification Of An Unusual Fold In Egf3.
Biochemistry V. 44 8782 2005
PubMed-ID: 15952784  |  Reference-DOI: 10.1021/BI050101F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VITAMIN K-DEPENDENT PROTEIN S
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentEGF MODULES 3 AND 4
    GenePROS1, PROS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:160 , GLU A:163 , ASN A:178 , ILE A:179BINDING SITE FOR RESIDUE CA A 246
2AC2SOFTWAREASP A:202 , GLU A:205 , ASN A:217 , TYR A:218BINDING SITE FOR RESIDUE CA A 247

(-) SS Bonds  (6, 6)

NMR Structure
No.Residues
1A:164 -A:176
2A:171 -A:185
3A:187 -A:200
4A:206 -A:215
5A:211 -A:224
6A:226 -A:241

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Z6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 13)

NMR Structure (13, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_046831E204GPROS_HUMANDisease (THPH5)  ---AE163G
02UniProtVAR_046832R233KPROS_HUMANPolymorphism41267007AR192K
03UniProtVAR_067302Y234CPROS_HUMANDisease (THPH6)387906675AY193C
04UniProtVAR_046833C241SPROS_HUMANDisease (THPH5)  ---AC200S
05UniProtVAR_046834D243NPROS_HUMANDisease (THPH5)  ---AD202N
06UniProtVAR_046835D245GPROS_HUMANDisease (THPH5)  ---AD204G
07UniProtVAR_046836C247GPROS_HUMANDisease (THPH5)  ---AC206G
08UniProtVAR_046837E249KPROS_HUMANDisease (THPH5)  ---AE208K
09UniProtVAR_005567N258SPROS_HUMANDisease (THPH5)121918473AN217S
10UniProtVAR_046838C265RPROS_HUMANDisease (THPH5)  ---AC224R
11UniProtVAR_046839C265WPROS_HUMANDisease (THPH5)  ---AC224W
12UniProtVAR_046840Y266CPROS_HUMANDisease (THPH5)777616039AY225C
13UniProtVAR_046841C267SPROS_HUMANDisease (THPH5)  ---AC226S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 7)

NMR Structure (4, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_3PS50026 EGF-like domain profile.PROS_HUMAN117-155
157-200
201-242
243-283
  2-
-
A:160-201
A:202-242
2ASX_HYDROXYLPS00010 Aspartic acid and asparagine hydroxylation site.PROS_HUMAN134-145
175-186
217-228
256-267
  2-
-
A:176-187
A:215-226
3EGF_2PS01186 EGF-like domain signature 2.PROS_HUMAN143-154
184-199
226-241
  1-
-
A:185-200
4EGF_CAPS01187 Calcium-binding EGF-like domain signature.PROS_HUMAN157-184
201-226
243-265
  2-
A:160-185
A:202-224

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003942361aENSE00001517824chr3:93692910-93692518393PROS_HUMAN1-26260--
1.5ENST000003942365ENSE00001595936chr3:93646251-93646094158PROS_HUMAN26-78530--
1.6ENST000003942366ENSE00001718413chr3:93643108-9364308425PROS_HUMAN79-8790--
1.7bENST000003942367bENSE00001597213chr3:93629549-9362946387PROS_HUMAN87-116300--
1.8bENST000003942368bENSE00001626925chr3:93624987-93624865123PROS_HUMAN116-157420--
1.9cENST000003942369cENSE00001142421chr3:93624759-93624628132PROS_HUMAN157-201451A:159-1602
1.10ENST0000039423610ENSE00001142413chr3:93619773-93619648126PROS_HUMAN201-243431A:160-20243
1.11ENST0000039423611ENSE00001142405chr3:93617413-93617292122PROS_HUMAN243-283411A:202-24241
1.12ENST0000039423612ENSE00001142399chr3:93615535-93615420116PROS_HUMAN284-322391A:243-2453
1.13ENST0000039423613ENSE00001142392chr3:93611966-93611777190PROS_HUMAN322-385640--
1.14ENST0000039423614ENSE00001142384chr3:93605347-93605180168PROS_HUMAN386-441560--
1.15ENST0000039423615ENSE00001215429chr3:93603740-93603572169PROS_HUMAN442-498570--
1.16ENST0000039423616ENSE00001303348chr3:93598158-93598007152PROS_HUMAN498-548510--
1.17ENST0000039423617ENSE00001329474chr3:93596035-93595810226PROS_HUMAN549-624760--
1.18bENST0000039423618bENSE00001291870chr3:93593249-935918811369PROS_HUMAN624-676530--

(-) Sequences/Alignments

NMR Structure
   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:87
 aligned with PROS_HUMAN | P07225 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:87
                                   209       219       229       239       249       259       269       279       
           PROS_HUMAN   200 KDVDECSLKPSICGTAVCKNIPGDFECECPEGYRYNLKSKSCEDIDECSENMCAQLCVNYPGGYTCYCDGKKGFKLAQDQKSCEVVS 286
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains -EGF_CA-1z6cA01 A:160-200                 --------------------------------------------- Pfam domains
         Sec.struct. author .................................eee....eee..hhhhhh....ee........ee.................... Sec.struct. author
             SAPs(SNPs) (1) ----G----------------------------KC------S-N-G-G-K--------S------RCS------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------W--------------------- SAPs(SNPs) (2)
                PROSITE (1) EEGF_3  PDB: A:160-201 UniProt: 201-242    EGF_3  PDB: A:202-242 UniProt: 243-283   --- PROSITE (1)
                PROSITE (2) -----------------ASX_HYDROXYL---------------------------ASX_HYDROXYL------------------- PROSITE (2)
                PROSITE (3) --------------------------EGF_2           -EGF_CA  PDB: A:202-224 --------------------- PROSITE (3)
                PROSITE (4) -EGF_CA  PDB: A:160-185    ------------------------------------------------------------ PROSITE (4)
           Transcript 1 (1) -Exon 1.10  PDB: A:160-202 UniProt: 201-243 ----------------------------------------1.1 Transcript 1 (1)
           Transcript 1 (2) 1.-----------------------------------------Exon 1.11  PDB: A:202-242                --- Transcript 1 (2)
                 1z6c A 159 KDVDECSLKPSICGTAVCKNIPGDFECECPEGYRYNLKSKSCEDIDECSENMCAQLCVNYPGGYTCYCDGKKGFKLAQDQKSCEVVS 245
                                   168       178       188       198       208       218       228       238       

   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  (0, 0)

(no "SCOP Domain" information available for 1Z6C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Z6C)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: EGF (60)

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain A   (PROS_HUMAN | P07225)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0030195    negative regulation of blood coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
    GO:0050819    negative regulation of coagulation    Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0017187    peptidyl-glutamic acid carboxylation    The gamma-carboxylation of peptidyl-glutamic acid; catalyzed by the vitamin K dependent gamma-glutamyl carboxylase.
    GO:0002576    platelet degranulation    The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
    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.
    GO:0006465    signal peptide processing    The proteolytic removal of a signal peptide from a protein during or after transport to a specific location in the cell.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0031093    platelet alpha granule lumen    The volume enclosed by the membrane of the platelet alpha granule.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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