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(-) Description

Title :  CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED ZPI IN I2 SPACE GROUP
 
Authors :  A. Zhou, Y. Yan, Z. Wei
Date :  23 Jan 12  (Deposition) - 09 Jan 13  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase Inhibitor, Serpin, Protein Z Dependent Inhibitor, Coagulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Huang, Y. Yan, Y. Tu, J. Gatti, G. J. J. Broze, A. Zhou, S. T. Olson
Structural Basis For Catalytic Activation Of Protein Z- Dependent Protease Inhibitor (Zpi) By Protein Z.
Blood V. 120 1726 2012
PubMed-ID: 22786881  |  Reference-DOI: 10.1182/BLOOD-2012-03-419598

(-) Compounds

Molecule 1 - PROTEIN Z DEPENDENT PROTEASE INHIBITOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSUMO3-HZPI-Y387R
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PSUMO3
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 23-408
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: REACTIVE LOOP CLEAVED ZPI
    Synonym: PZ-DEPENDENT PROTEASE INHIBITOR, PZI, SERPIN A10
 
Molecule 2 - PROTEIN Z DEPENDENT PROTEASE INHIBITOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSUMO3-HZPI-Y387R
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Expression System Vector: PSUMO3
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 409-444
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: REACTIVE LOOP CLEAVED ZPI
    Synonym: PZ-DEPENDENT PROTEASE INHIBITOR, PZI, SERPIN A10

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NA2Ligand/IonSODIUM ION
3PO43Ligand/IonPHOSPHATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:292BINDING SITE FOR RESIDUE NA A1387
2AC2SOFTWAREASN A:159 , ARG A:163BINDING SITE FOR RESIDUE CA A1388
3AC3SOFTWARESER A:64 , ARG A:67BINDING SITE FOR RESIDUE PO4 A1389
4AC4SOFTWAREGLU A:100 , LYS A:104 , PRO A:117 , GLY A:118 , LEU A:120 , PRO A:121BINDING SITE FOR RESIDUE PO4 A1390
5AC5SOFTWAREGLN A:102BINDING SITE FOR RESIDUE NA A1391
6AC6SOFTWAREHIS A:73 , GLY A:75 , ASN A:76 , GLN A:323BINDING SITE FOR RESIDUE PO4 A1392

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AFX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4AFX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (9, 9)

Asymmetric/Biological Unit (9, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020326S61GZPI_HUMANPolymorphism941591AS40G
2UniProtVAR_038833G139RZPI_HUMANPolymorphism56137907AG118R
3UniProtVAR_051940L158QZPI_HUMANPolymorphism2232699AL137Q
4UniProtVAR_020327T161SZPI_HUMANPolymorphism2232700AT140S
5UniProtVAR_051941R196HZPI_HUMANPolymorphism2232701AR175H
6UniProtVAR_038834G271SZPI_HUMANPolymorphism2232708AG250S
7UniProtVAR_038835Q384PZPI_HUMANPolymorphism  ---AQ363P
8UniProtVAR_051942Q384RZPI_HUMANPolymorphism2232710AQ363R
9UniProtVAR_070192F420LZPI_HUMANPolymorphism546304706BF399L
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AFX)

(-) Exons   (0, 0)

(no "Exon" information available for 4AFX)

(-) 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:347
 aligned with ZPI_HUMAN | Q9UK55 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:347
                                    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       370       380       390       400       
            ZPI_HUMAN    61 SEEEKAWLMASRQQLAKETSNFGFSLLRKISMRHDGNMVFSPFGMSLAMTGLMLGATGPTETQIKRGLHLQALKPTKPGLLPSLFKGLRETLSRNLELGLTQGSFAFIHKDFDVKETFFNLSKRYFDTECVPMNFRNASQAKRLMNHYINKETRGKIPKLFDEINPETKLILVDYILFKGKWLTPFDPVFTEVDTFHLDKYKTIKVPMMYGAGKFASTFDKNFRCHVLKLPYQGNATMLVVLMEKMGDHLALEDYLTTDLVETWLRNMKTRNMEVFFPKFKLDQKYEMHELLRQMGIRRIFSPFADLSELSATGRNLQVSRVLQRTVIEVDERGTEAVAGILSEITA 407
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhh...hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.....hhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhhhh..............eeeeeeeeeeeeee.....hhhhheeeeee.....eeeeeeeeeeeeeeeeee....eeeeeee....eeeeeeee.......hhhhh.hhhhhhhhhhh.eeeeeeeeee.eeeeeeeehhhhhhhh..hhhhh...............eeeeeeeeeeeee...eeeeeeeeeeeee. Sec.struct. author
             SAPs(SNPs) (1) G-----------------------------------------------------------------------------R------------------Q--S----------------------------------H--------------------------------------------------------------------------S----------------------------------------------------------------------------------------------------------------P----------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4afx A  40 SEEEKAWLMASRQQLAKETSNFGFSLLRKISMRHDGNMVFSPFGMSLAMTGLMLGATGPTETQIKRGLHLQALKPTKPGLLPSLFKGLRETLSRNLELGLTQGSFAFIHKDFDVKETFFNLSKRYFDTECVPMNFRNASQAKRLMNHYINKETRGKIPKLFDEINPETKLILVDYILFKGKWLTPFDPVFTEVDTFHLDKYKTIKVPMMYGAGKFASTFDKNFRCHVLKLPYQGNATMLVVLMEKMGDHLALEDYLTTDLVETWLRNMKTRNMEVFFPKFKLDQKYEMHELLRQMGIRRIFSPFADLSELSATGRNLQVSRVLQRTVIEVDERGTEAVAGILSEITA 386
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       


Chain B from PDB  Type:PROTEIN  Length:34
 aligned with ZPI_HUMAN | Q9UK55 from UniProtKB/Swiss-Prot  Length:444

    Alignment length:34
                                   420       430       440    
            ZPI_HUMAN   411 PPVIKVDRPFHFMIYEETSGMLLFLGRVVNPTLL 444
               SCOP domains ---------------------------------- SCOP domains
               CATH domains ---------------------------------- CATH domains
               Pfam domains ---------------------------------- Pfam domains
         Sec.struct. author ..eee....eeeeeee....eeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------L------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------- PROSITE
                 Transcript ---------------------------------- Transcript
                 4afx B 390 PPVIKIDRPFHFMIYEETSGMLLFLGRVVNPTLL 423
                                   399       409       419
   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 4AFX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AFX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AFX)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ZPI_HUMAN | Q9UK55)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    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:0007599    hemostasis    The stopping of bleeding (loss of body fluid) or the arrest of the circulation to an organ or part.
    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:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0060046    regulation of acrosome reaction    Any process that modulates the frequency, rate or extent of the acrosome reaction.
cellular component
    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.

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  4afx
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 Related Entries

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

UniProtKB/Swiss-Prot
        ZPI_HUMAN | Q9UK55: 3f1s 3h5c 4aju

(-) Related Entries Specified in the PDB File

4aju CRYSTAL STRUCTURE OF THE REACTIVE LOOP CLEAVED ZPI IN P41 SPACE GROUP