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(-) Description

Title :  DISSECTING AND DESIGNING INHIBITOR SELECTIVITY DETERMINANTS AT THE S1 SITE USING AN ARTIFICIAL ALA190 PROTEASE (ALA190 UPA)
 
Authors :  B. A. Katz, C. Luong, J. D. Ho, J. R. Somoza, E. Gjerstad, J. Tang, S. R. Williams, E. Verner, R. L. Mackman, W. B. Young, P. A. Sprengeler, H. Chan, K. Mortara, J. W. Janc, M. E. Mcgrath
Date :  09 Sep 03  (Deposition) - 21 Sep 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Srcr, Scavenger Receptor Cysteine-Rich Domain, Serine Protease Ala190 Upa, S1 Site, Selectivity, Conserved Water Displacement Hydrogen Bond Deficit, Trypsin, Thrombin, Hepsin, Factor Viia, Serine Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. A. Katz, C. Luong, J. D. Ho, J. R. Somoza, E. Gjerstad, J. Tang, S. R. Williams, E. Verner, R. L. Mackman, W. B. Young, P. A. Sprengeler, H. Chan, K. Mortara, J. W. Janc, M. E. Mcgrath
Dissecting And Designing Inhibitor Selectivity Determinants At The S1 Site Using An Artificial Ala190 Protease (Ala190 Upa).
J. Mol. Biol. V. 344 527 2004
PubMed-ID: 15522303  |  Reference-DOI: 10.1016/J.JMB.2004.09.032
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERINE PROTEASE HEPSIN
    ChainsL
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    Expression System VariantKM71
    FragmentLIGHT CHAIN
    GeneHPN OR TMPRSS1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRANSMEMBRANE PROTEASE, SERINE 1
 
Molecule 2 - SERINE PROTEASE HEPSIN
    ChainsH
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Taxid4922
    Expression System VariantKM71
    FragmentHEAVY CHAIN (CATALYTIC DOMAIN)
    GeneHPN OR TMPRSS1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTRANSMEMBRANE PROTEASE, SERINE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CR91Ligand/Ion2-{5-[AMINO(IMINIO)METHYL]-6-FLUORO-1H-BENZIMIDAZOL-2-YL}-6-[(2-METHYLCYCLOHEXYL)OXY]BENZENOLATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU H:41 , HIS H:57 , CYS H:58 , PRO H:60 , ASP H:189 , ALA H:190 , CYS H:191 , SER H:195 , VAL H:213 , TRP H:215 , GLY H:219 , GLY H:226 , HOH H:270 , HOH H:276 , HOH H:355 , HOH H:390BINDING SITE FOR RESIDUE CR9 H 256

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1H:42 -H:58
2H:136 -H:201
3H:168 -H:182
4H:191 -H:220
5L:32 -L:95
6L:45 -L:105
7L:74 -L:93
8L:108 -H:122

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1O5F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1O5F)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.HEPS_HUMAN163-405  1H:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.HEPS_HUMAN199-204  1H:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.HEPS_HUMAN347-358  1H:189-200

(-) Exons   (10, 11)

Asymmetric/Biological Unit (10, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003922261ENSE00001114495chr19:35531410-3553144940HEPS_HUMAN-00--
1.2aENST000003922262aENSE00001638672chr19:35532626-35532776151HEPS_HUMAN-00--
1.2cENST000003922262cENSE00001669183chr19:35533357-3553342670HEPS_HUMAN1-660--
1.3ENST000003922263ENSE00000953257chr19:35540194-35540295102HEPS_HUMAN6-40350--
1.4ENST000003922264ENSE00001253027chr19:35540379-3554042042HEPS_HUMAN40-54151-
L:5-9
-
5
1.5ENST000003922265ENSE00001253082chr19:35550577-35550706130HEPS_HUMAN54-97441-
L:9-52
-
44
1.6ENST000003922266ENSE00000953258chr19:35550778-35550900123HEPS_HUMAN97-138421-
L:52-93
-
42
1.7ENST000003922267ENSE00000862744chr19:35551033-3555107341HEPS_HUMAN138-152151-
L:93-107
-
15
1.8ENST000003922268ENSE00000700403chr19:35551251-35551416166HEPS_HUMAN152-207562H:16-61 (gaps)
L:107-114
46
8
1.9ENST000003922269ENSE00000953259chr19:35551531-35551721191HEPS_HUMAN207-271651H:61-116 (gaps)
-
67
-
1.10ENST0000039222610ENSE00000700401chr19:35556154-3555624996HEPS_HUMAN271-303331H:116-148
-
33
-
1.11ENST0000039222611ENSE00000700399chr19:35556443-35556585143HEPS_HUMAN303-350481H:148-192 (gaps)
-
51
-
1.12ENST0000039222612ENSE00001253074chr19:35556772-35556936165HEPS_HUMAN351-405551H:193-243 (gaps)
-
56
-
1.13ENST0000039222613ENSE00001114496chr19:35557153-35557475323HEPS_HUMAN406-417121H:244-255
-
12
-

(-) 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 H from PDB  Type:PROTEIN  Length:248
 aligned with HEPS_HUMAN | P05981 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:255
                                   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     
          HEPS_HUMAN    163 IVGGRDTSLGRWPWQVSLRYDGAHLCGGSLLSGDWVLTAAHCFPERNRVLSRWRVFAGAVAQASPHGLQLGVQAVVYHGGYLPFRDPNSEENSNDIALVHLSSPLPLTEYIQPVCLPAAGQALVDGKICTVTGWGNTQYYGQQAGVLQEARVPIISNDVCNGADFYGNQIKPKMFCAGYPEGGIDACQGDSGGPFVCEDSISRTPRWRLCGIVSWGTGCALAQKPGVYTKVSDFREWIFQAIKTHSEASGMVTQL  417
               SCOP domains d1o5fh_ H: Hepsin, catalytic domain                                                                                                                                                                                                                             SCOP domains
               CATH domains 1o5fH01     1o5fH02 H:28-120,H:231-255 Trypsin-like serine proteases                                             1o5fH01 H:16-27,H:121-230 Trypsin-like serine proteases                                                              1o5fH02                   CATH domains
               Pfam domains Trypsin-1o5fH01 H:16-238                                                                                                                                                                                                                      ----------------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeee....eeeehhhhhhhhhhhhh.eeeee..........eee.eeeeeee......-------.....eeeee..........................eeeeee..............eeeeeeeehhhhhh............eeee................eeeeee......eeeeeeeeee..........eeeee...hhhhhhhhhhhhh...eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: H:16-243 UniProt: 163-405                                                                                                                                                                                                        ------------ PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ----------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.8  PDB: H:16-61 (gaps) [INCOMPLETE]   ---------------------------------------------------------------Exon 1.10  PDB: H:116-148        -----------------------------------------------Exon 1.12  PDB: H:193-243 (gaps) UniProt: 351-405      Exon 1.13    Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.9  PDB: H:61-116 (gaps) UniProt: 207-271                  -------------------------------Exon 1.11  PDB: H:148-192 (gaps)                ------------------------------------------------------------------- Transcript 1 (2)
                1o5f H   16 IVGGRDTSLGRWPWQVSLRYDGAHLCGGSLLSGDWVLTAAHCFPERNRVLSRWRVFAGAVAQASPHGLQLGVQAVVYHGGYLPF-------NSNDIALVHLSSPLPLTEYIQPVCLPAAGQALVDGKICTVTGWGNTQYYGQQAGVLQEARVPIISNDVCNGADFYGNQIKPKMFCAGYPEGGIDACQGDSGGPFVCEDSISRTPRWRLCGIVSWGTGCALAQKPGVYTKVSDFREWIFQAIKTHSEASGMVTQL  255
                                    25        35|       46        56       65A||||    71      ||83        93   |     - |     107       117       127       137       147||     158       168       176       185 ||||  194       204    |||210      |221|      230       240       250     
                                              35|                          65A||||           78|              97      99                                              148|                      175A|      184A  ||||                208A|||      217|  |                                  
                                               37                           65B|||            81                                                                       150                       175B         186A|||                 208B||       219  |                                  
                                                                             65C||                                                                                                                             186B||                  208C|         221A                                  
                                                                              65D|                                                                                                                              186C|                   208D                                               
                                                                               65E                                                                                                                                189                                                                      

Chain L from PDB  Type:PROTEIN  Length:110
 aligned with HEPS_HUMAN | P05981 from UniProtKB/Swiss-Prot  Length:417

    Alignment length:110
                                    59        69        79        89        99       109       119       129       139       149       159
          HEPS_HUMAN     50 PLYPVQVSSADARLMVFDKTEGTWRLLCSSRSNARVAGLSCEEMGFLRALTHSELDVRTAGANGTSGFFCVDEGRLPHTQRLLEVISVCDCPRGRFLAAICQDCGRRKLP  159
               SCOP domains d1o5fl_ L: Hepsin, N-terminal domain                                                                           SCOP domains
               CATH domains 1o5fL00 L:5-114 Mac-2 Binding Protein;                                                                         CATH domains
               Pfam domains Hepsin-SRCR-1o5fL01 L:5-114                                                                                    Pfam domains
         Sec.struct. author ....eee......eeeee....eeeee....hhhhhhhhhhhhhh...eeeeeeeehhhhh......eeee...hhhhh.hhhh.eeee.....eeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1.4  ------------------------------------------Exon 1.6  PDB: L:52-93 UniProt: 97-138    -------------Exon 1.8 Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.5  PDB: L:9-52 UniProt: 54-97        ----------------------------------------Exon 1.7       ------- Transcript 1 (2)
                1o5f L    5 PLYPVQVSSADARLMVFDKTEGTWRLLCSSRSNARVAGLSCEEMGFLRALTHSELDVRTAGAAGTSGFFCVDEGRLPHTQRLLEVISVCDCPRGRFLAAICQDCGRRKLP  114
                                    14        24        34        44        54        64        74        84        94       104       114

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain H,L   (HEPS_HUMAN | P05981)
molecular function
    GO:0015269    calcium-activated potassium channel activity    Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient.
    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: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: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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0070008    serine-type exopeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the N- or C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0034769    basement membrane disassembly    The controlled breakdown of the basement membrane in the context of a normal process such as imaginal disc eversion.
    GO:0090103    cochlea morphogenesis    The process in which the cochlea is generated and organized.
    GO:0050910    detection of mechanical stimulus involved in sensory perception of sound    The series of events involved in the perception of sound vibration in which the vibration is received and converted into a molecular signal.
    GO:0048012    hepatocyte growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands.
    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:0050680    negative regulation of epithelial cell proliferation    Any process that stops, prevents or reduces the rate or extent of epithelial cell proliferation.
    GO:0010719    negative regulation of epithelial to mesenchymal transition    Any process that decreases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0097195    pilomotor reflex    The reflex process in which the arrectores pilorum (hair follicle) muscles contract and cause the hair to stand erect.
    GO:0043923    positive regulation by host of viral transcription    Any process in which a host organism activates or increases the frequency, rate or extent of viral transcription, the synthesis of either RNA on a template of DNA or DNA on a template of RNA.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:2000347    positive regulation of hepatocyte proliferation    Any process that activates or increases the frequency, rate or extent of hepatocyte proliferation.
    GO:0010756    positive regulation of plasminogen activation    Any process that increases the rate, frequency or extent of plasminogen activation. Plasminogen activation is the process in which plasminogen is processed to plasmin.
    GO:2000611    positive regulation of thyroid hormone generation    Any process that activates or increases the frequency, rate or extent of thyroid hormone generation.
    GO:0071805    potassium ion transmembrane transport    A process in which a potassium ion is transported from one side of a membrane to the other.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0097066    response to thyroid hormone    A change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
cellular component
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    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
        HEPS_HUMAN | P059811o5e 1p57 1z8g 3t2n 5ce1

(-) Related Entries Specified in the PDB File

1p57 THE SAME PROTEASE WITH A RELATED INHIBITOR