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(-) Description

Title :  BOVINE THROMBIN-ACTIVATABLE FIBRINOLYSIS INHIBITOR (TAFIA) IN COMPLEX WITH TICK-DERIVED CARBOXYPEPTIDASE INHIBITOR.
 
Authors :  L. Sanglas, Z. Valnickova, J. L. Arolas, I. Pallares, T. Guevara, M. Sol T. Kristensen, J. J. Enghild, F. X. Aviles, F. X. Gomis-Ruth
Date :  15 May 08  (Deposition) - 19 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protease-Inhibitor Complex, Carboxypeptidase, Glycoprotein, Hydrolase, Metal-Binding, Metalloprotease, Protease, Secreted, Zymogen, Blood Coagulation, Fibrinolysis, Metalloenzyme Inhibitor, Metalloprotease Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Sanglas, Z. Valnickova, J. L. Arolas, I. Pallares, T. Guevara, M. Sola, T. Kristensen, J. J. Enghild, F. X. Aviles, F. X. Gomis-Ruth
Structure Of Activated Thrombin-Activatable Fibrinolysis Inhibitor, A Molecular Link Between Coagulation And Fibrinolysis.
Mol. Cell V. 31 598 2008
PubMed-ID: 18722183  |  Reference-DOI: 10.1016/J.MOLCEL.2008.05.031
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE B2
    Chains: A
    EC Number: 3.4.17.20
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Synonym: TAFIA
    Tissue: BLOOD
 
Molecule 2 - CARBOXYPEPTIDASE INHIBITOR
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAT-4-OMPA-TCI
    Expression System Strain: BL21/DE3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: RHIPICEPHALUS BURSA
    Organism Taxid: 67831
    Synonym: TICK CARBOXYPEPTIDASE INHIBITOR, TCI

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2SO45Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , LEU B:74BINDING SITE FOR RESIDUE ZN A 309
2AC2SOFTWAREHIS A:69 , ARG A:127 , ASN A:144 , ARG A:145 , TYR A:248 , LEU B:74BINDING SITE FOR RESIDUE ACT A 601
3AC3SOFTWAREPRO A:46 , LEU A:47 , TYR A:48 , PRO A:109BINDING SITE FOR RESIDUE ACT A 602
4AC4SOFTWARESER A:157 , SER A:158 , ARG B:52BINDING SITE FOR RESIDUE SO4 A 603
5AC5SOFTWARETYR A:208 , SER A:209 , SER A:211 , HIS A:1501BINDING SITE FOR RESIDUE SO4 A 604
6AC6SOFTWAREHIS A:216 , SER A:220 , ARG A:224BINDING SITE FOR RESIDUE SO4 A 605
7AC7SOFTWARESER A:14 , ASN A:16BINDING SITE FOR RESIDUE SO4 A 606
8AC8SOFTWARELYS A:135 , ASN A:136 , ALA A:137 , SER A:160 , CYS A:161BINDING SITE FOR RESIDUE SO4 A 607

(-) SS Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1A:66 -A:79
2A:138 -A:161
3A:152 -A:166
4B:3 -B:31
5B:10 -B:27
6B:16 -B:32
7B:40 -B:70
8B:47 -B:64
9B:54 -B:71

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:197 -Tyr A:198
2Pro A:205 -Tyr A:206
3Arg A:272 -Asp A:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3D4U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D4U)

(-) Exons   (0, 0)

(no "Exon" information available for 3D4U)

(-) 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:296
 aligned with CBPB2_BOVIN | Q2KIG3 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:306
                                   127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417      
         CBPB2_BOVIN    118 SYYEQYHSLNEIYSWIEVMTERYPDMVEKIHIGSSYEKYPLYVLKVSKKEQRAKNAMWIDCGIHAREWISPAFCLWFVGSVTYYYGKEKMHTNLLKHMDFYIMPVVNVDGYDYTWKKDRMWRKNRSLHEKNACVGTDLNRNFASKHWCGEGASSSSCSEIYCGTYPESEPEVKAVADFLRRNIKHIKAYISMHSYSQKIVFPYSYSRSRSKDHEELSLVAREAVFAMENIHRNIRYTHGSGSESLYLAPGGSDDWIYDLGIKYSFTFELRDKGKYGFLLPESYIRPTCSEALVAVAKIASHVVKNV  423
               SCOP domains d3d4ua_ A: automated matches                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 3d4uA00 A:7-308 Zn peptidases                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh..hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee..-----..eeeee.......hhhhhhhhhhhhhhhhh...-----......eeeee...hhhhhhhhhhh...................hhhhh...........................hhhhhhhhhhhhhh...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhhhh.....eeeehhhhh.....hhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                3d4u A    7 SYYEQYHSLNEIYSWIEVMTERYPDMVEKIHIGSSYEKYPLYVLKVSK-----KNAMWIDCGIHAREWISPAFCLWFVGSVTYYYGK-----NLLKHMDFYIMPVVNVDGYDYTWKKDRMWRKNRSLHEKNACVGTDLNRNFASKHWCGEGASSSSCSEIYCGTYPESEPEVKAVADFLRRNIKHIKAYISMHSYSQKIVFPYSYSRSRSKDHEELSLVAREAVFAMENIHRNIRYTHGSGSESLYLAPGGSDDWIYDLGIKYSFTFELRDKGKYGFLLPESYIRPTCSEALVAVAKIASHVVKNV  308
                                    16        26        36        46       | -   |    65        75        85      |  -  |    105       115       125       135       145    |||154       164       174       184   ||| 193       203       213       223       233 |||   242       252       262       272       282       292       302      
                                                                          54    59                               92    98                                                 150||                                  188||                                           235||                                                                        
                                                                                                                                                                          1501|                                  1889|                                           2356|                                                                        
                                                                                                                                                                            151                                    189                                             236                                                                        


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with TCI1_RHIBU | Q5EPH2 from UniProtKB/Swiss-Prot  Length:97

    Alignment length:74
                                    32        42        52        62        72        82        92    
          TCI1_RHIBU     23 NECVSKGFGCLPQSDCPQEARLSYGGCSTVCCDLSKLTGCKGKGGECNPLDRQCKELQAESASCGKGQKCCVWL   96
               SCOP domains d3d4ub1 B:1-37                       d3d4ub2 B:38-74                       SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeehhhhhhhh.ee.......eee.hhhh..hhhhh.eeee.......hhhhhhhhh..eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                3d4u B    1 NECVSKGFGCLPQSDCPQEARLSYGGCSTVCCDLSKLTGCKGKGGECNPLDRQCKELQAESASCGKGQKCCVWL   74
                                    10        20        30        40        50        60        70
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3D4U)

(-) Gene Ontology  (21, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPB2_BOVIN | Q2KIG3)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004181    metallocarboxypeptidase activity    Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

Chain B   (TCI1_RHIBU | Q5EPH2)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    GO:0008191    metalloendopeptidase inhibitor activity    Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0044002    acquisition of nutrients from host    The process that begins with the production and formation of structures and molecules in an organism that are required for the acquisition and utilization of nutrients from its host organism, and the ends with the acquirement of the nutrients. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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: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.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBPB2_BOVIN | Q2KIG3: 3dgv 3osl
        TCI1_RHIBU | Q5EPH2: 1zlh 1zli 2jto 2k2x 2k2y 2k2z 3lms 3osl

(-) Related Entries Specified in the PDB File

1kwm HUMAN PROCARBOXYPEPTIDASE B
1zli HUMAN CARBOXYPEPTIDASE B IN COMPLEX WITH TICK-DERIVED CARBOXYPEPTIDASE INHIBITOR