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(-) Description

Title :  HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETION MUTANT] COMPLEXED WITH PEPTIDE N-ACETYL-TEAAAGDGGVMTGR-OH
 
Authors :  D. A. Di Giusto, A. P. Sutherland, L. Jankova, S. J. Harrop, P. M. Curmi,
Date :  21 Aug 05  (Deposition) - 11 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,P
Keywords :  Serpin, Peptide Binding, Inhibitor, Hydrolase Inhibitor-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. A. Di Giusto, A. P. Sutherland, L. Jankova, S. J. Harrop, P. M. Curmi G. C. King
Plasminogen Activator Inhibitor-2 Is Highly Tolerant To P8 Residue Substitution--Implications For Serpin Mechanistic Model And Prediction Of Nssnp Activities
J. Mol. Biol. V. 353 1069 2005
PubMed-ID: 16214170  |  Reference-DOI: 10.1016/J.JMB.2005.09.008

(-) Compounds

Molecule 1 - PLASMINOGEN ACTIVATOR INHIBITOR-2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPAI-2, PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR, MONOCYTE ARG-SERPIN, UROKINASE INHIBITOR
 
Molecule 2 - 14-MER FROM PLASMINOGEN ACTIVATOR INHIBITOR-2
    ChainsP
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPAI-2, PLACENTAL PLASMINOGEN ACTIVATOR INHIBITOR, MONOCYTE ARG-SERPIN, UROKINASE INHIBITOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:206 , TRP A:208 , VAL A:362 , ASN A:363 , GLU A:365 , THR P:345BINDING SITE FOR RESIDUE ACE P 344
2AC2SOFTWARESER A:31 , SER A:34 , ILE A:35 , THR A:38 , LYS A:180 , ILE A:181 , LEU A:184 , SER A:189 , ASP A:193 , THR A:194 , ARG A:195 , MET A:196 , VAL A:197 , LEU A:198 , VAL A:199 , ASN A:200 , ALA A:201 , VAL A:202 , TYR A:203 , PHE A:204 , LYS A:205 , GLY A:206 , TRP A:208 , TYR A:258 , LYS A:335 , ALA A:338 , PHE A:340 , ASN A:347 , ASP A:348 , LEU A:349 , PHE A:350 , LEU A:351 , SER A:352 , GLU A:353 , VAL A:354 , PHE A:355 , HIS A:356 , GLN A:357 , ALA A:358 , MET A:359 , VAL A:360 , ASP A:361 , HOH A:439 , HOH A:546 , HOH P:136 , HOH P:188 , HOH P:246 , HOH P:275 , ACE P:344BINDING SITE FOR CHAIN P OF 14-MER FROM PLASMINOGEN ACTIVATOR INHIBITOR-2

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:405

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ARQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011743N120DPAI2_HUMANPolymorphism6098AN120D
2UniProtVAR_014173R229HPAI2_HUMANPolymorphism6100AR229H
3UniProtVAR_051946G374APAI2_HUMANPolymorphism34066931PG352A
4UniProtVAR_011744N404KPAI2_HUMANPolymorphism6103AN404K
5UniProtVAR_011745S413CPAI2_HUMANPolymorphism6104AS413C

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.PAI2_HUMAN388-398  1A:388-398

(-) Exons   (7, 8)

Asymmetric/Biological Unit (7, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002995022aENSE00001913834chr18:61554934-6155500471PAI2_HUMAN-00--
1.5ENST000002995025ENSE00001743384chr18:61558670-61558846177PAI2_HUMAN1-56561A:3-56
-
54
-
1.7ENST000002995027ENSE00001591590chr18:61562498-61562617120PAI2_HUMAN57-96401A:57-62
-
6
-
1.8cENST000002995028cENSE00001102622chr18:61564325-61564453129PAI2_HUMAN97-139431A:101-139
-
39
-
1.9bENST000002995029bENSE00002141382chr18:61564961-61565078118PAI2_HUMAN140-179401A:140-179
-
40
-
1.10ENST0000029950210ENSE00002158595chr18:61568974-61569116143PAI2_HUMAN179-226481A:179-226 (gaps)
-
48
-
1.11bENST0000029950211bENSE00002169488chr18:61569638-61569802165PAI2_HUMAN227-281551A:227-281 (gaps)
-
55
-
1.12bENST0000029950212bENSE00001812472chr18:61570135-61571124990PAI2_HUMAN282-4151342A:282-415 (gaps)
P:344-358
134
15

(-) 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:360
 aligned with PAI2_HUMAN | P05120 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:413
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412   
           PAI2_HUMAN     3 DLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMAKVLQFNEVGANAVTPMTPENFTSCGFMQQIQKGSYPDAILQAQAADKIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKLNGLYPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPDEIADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEGTEAAAGTGGVMTGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP 415
               SCOP domains d2arqa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2arqA01 A:3-207,A:310-364 Antithrombin, subunit I, domain 2                                                                                                                                                  2arqA02 A  :208-309,A:382-411 Alpha-1-antitrypsin, domain 1                                           2arqA01 A:3-207,A:310-364                              --           ----2arqA02 A:208-309,A:382-411   ---- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhh....--------------------------------------.hhhhhhhhhhhhhhh.....eeeeeeeeeee.....hhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhh................eeeeeeeeeeeee......ee..--.eeeeee..eeeee.eeeeeeeeeeeeehhh.eeeeeee....eeeeeeee.--......hhhhhhhhhhhhhhhhhh....eeeeeeeeee.eeeeeeeehhhhhhhhh.hhhhh..............eeeeeeeeeeeeee....-----------.........eee....eeeeeee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------D------------------------------------------------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K--------C-- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     ----------------- PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:3-56 UniProt: 1-56 [INCOMPLETE]      Exon 1.7  PDB: A:57-62 UniProt: 57-96   Exon 1.8c  PDB: A:101-139 UniProt: 97-139  ---------------------------------------Exon 1.10  PDB: A:179-226 (gaps)                Exon 1.11b  PDB: A:227-281 (gaps) UniProt: 227-281     Exon 1.12b  PDB: A:282-415 (gaps) UniProt: 282-415                                                                                     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:140-179               -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2arq A   3 DLCVANTLFALNLFKHLAKASPTQNLFLSPWSISSTMAMVYMGSRGSTEDQMASVLQFNE--------------------------------------DKIHSSFRSLSSAINASTGNYLLESVNKLFGEKSASFREEYIRLCQKYYSSEPQAVDFLECAEEARKKINSWVKTQTKGKIPNLLPEGSVDGDTRMVLVNAVYFKGKWKTPFEKKL--LFPFRVNSAQRTPVQMMYLREKLNIGYIEDLKAQILELPYAGDVSMFLLLPD--ADVSTGLELLESEITYDKLNKWTSKDKMAEDEVEVYIPQFKLEEHYELRSILRSMGMEDAFNKGRANFSGMSERNDLFLSEVFHQAMVDVNEEG-----------TGRTGHGGPQFVADHPFLFLIMHKITNCILFFGRFSSP 415
                                    12        22        32        42        52        62         -         -         -       102       112       122       132       142       152       162       172       182       192       202       212   |  |222       232       242       252       262       | -|      282       292       302       312       322       332       342       352       362   |     -     | 382       392       402       412   
                                                                                      62                                    101                                                                                                                216  |                                                270  |                                                                                          366         378                                     
                                                                                                                                                                                                                                                  219                                                   273                                                                                                                                              

Chain P from PDB  Type:PROTEIN  Length:15
 aligned with PAI2_HUMAN | P05120 from UniProtKB/Swiss-Prot  Length:415

    Alignment length:15
                                   375     
           PAI2_HUMAN   366 GTEAAAGTGGVMTGR 380
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------A------ SAPs(SNPs)
                    PROSITE --------------- PROSITE
           Transcript 1 (1) Exon 1.12b      Transcript 1 (1)
           Transcript 1 (2) --------------- Transcript 1 (2)
                 2arq P 344 xTEAAAGDGGVMTGR 358
                            |      353     
                          344-ACE          

   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/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,P   (PAI2_HUMAN | P05120)
molecular function
    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:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    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:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PAI2_HUMAN | P051201by7 1jrr 2arr

(-) Related Entries Specified in the PDB File

1jrr HUMAN PLASMINOGEN ACTIVATOR INHIBITOR-2.[LOOP (66-98) DELETION MUTANT] COMPLEXED WITH PEPTIDE MIMICKING THE REACTIVE CENTER LOOP
2arr THE SAME PROTEIN, MUTATION T8M AT 1.55 A