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(-) Description

Title :  SUBSTRATE INDUCED REMODELING OF THE ACTIVE SITE REGULATES HTRA1 ACTIVITY
 
Authors :  L. Truebestein, A. Tennstaedt, P. Hauske, T. Krojer, M. Kaiser, T. Clau M. Ehrmann
Date :  11 Jul 10  (Deposition) - 23 Feb 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  A,B,C  (2x)
Keywords :  Serine Protease, Degp, Htra, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Truebestein, A. Tennstaedt, T. Monig, T. Krojer, F. Canellas, M. Kaiser, T. Clausen, M. Ehrmann
Substrate-Induced Remodeling Of The Active Site Regulates Human Htra1 Activity.
Nat. Struct. Mol. Biol. V. 18 386 2011
PubMed-ID: 21297635  |  Reference-DOI: 10.1038/NSMB.2013

(-) Compounds

Molecule 1 - SERINE PROTEASE HTRA1
    ChainsA, B, C
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentHTRA1 PROTEASE DOMAIN (UNP RESIDUES 158-375)
    GeneHTRA, HTRA1, PRSS11
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymL56, SERINE PROTEASE 11

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)ABC
Biological Unit 2 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:218 , HIS A:220 , ASP A:250 , THR A:344 , LEU A:345BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREASN B:218 , HIS B:220 , ASP B:250 , THR B:344 , LEU B:345 , LYS B:346BINDING SITE FOR RESIDUE SO4 B 2
3AC3SOFTWARELYS A:346 , ASN C:218 , HIS C:220 , ASP C:250 , THR C:344 , LEU C:345BINDING SITE FOR RESIDUE SO4 C 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NWU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NWU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 24)

Asymmetric Unit (8, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076376R166LHTRA1_HUMANDisease (CADASIL2)864622781A/B/CR166L
2UniProtVAR_076377A173PHTRA1_HUMANDisease (CADASIL2)  ---A/B/CA173P
3UniProtVAR_063148A252THTRA1_HUMANDisease (CARASIL)113993968A/B/CA252T
4UniProtVAR_076378S284GHTRA1_HUMANDisease (CADASIL2)  ---A/B/CS284G
5UniProtVAR_076379S284RHTRA1_HUMANDisease (CADASIL2)864622782A/B/CS284R
6UniProtVAR_076380P285QHTRA1_HUMANDisease (CADASIL2)  ---A/B/CP285Q
7UniProtVAR_076381F286VHTRA1_HUMANDisease (CADASIL2)  ---A/B/CF286V
8UniProtVAR_063149V297MHTRA1_HUMANDisease (CARASIL)113993969A/B/CV297M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 24)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076376R166LHTRA1_HUMANDisease (CADASIL2)864622781A/B/CR166L
2UniProtVAR_076377A173PHTRA1_HUMANDisease (CADASIL2)  ---A/B/CA173P
3UniProtVAR_063148A252THTRA1_HUMANDisease (CARASIL)113993968A/B/CA252T
4UniProtVAR_076378S284GHTRA1_HUMANDisease (CADASIL2)  ---A/B/CS284G
5UniProtVAR_076379S284RHTRA1_HUMANDisease (CADASIL2)864622782A/B/CS284R
6UniProtVAR_076380P285QHTRA1_HUMANDisease (CADASIL2)  ---A/B/CP285Q
7UniProtVAR_076381F286VHTRA1_HUMANDisease (CADASIL2)  ---A/B/CF286V
8UniProtVAR_063149V297MHTRA1_HUMANDisease (CARASIL)113993969A/B/CV297M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (8, 48)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_076376R166LHTRA1_HUMANDisease (CADASIL2)864622781A/B/CR166L
2UniProtVAR_076377A173PHTRA1_HUMANDisease (CADASIL2)  ---A/B/CA173P
3UniProtVAR_063148A252THTRA1_HUMANDisease (CARASIL)113993968A/B/CA252T
4UniProtVAR_076378S284GHTRA1_HUMANDisease (CADASIL2)  ---A/B/CS284G
5UniProtVAR_076379S284RHTRA1_HUMANDisease (CADASIL2)864622782A/B/CS284R
6UniProtVAR_076380P285QHTRA1_HUMANDisease (CADASIL2)  ---A/B/CP285Q
7UniProtVAR_076381F286VHTRA1_HUMANDisease (CADASIL2)  ---A/B/CF286V
8UniProtVAR_063149V297MHTRA1_HUMANDisease (CARASIL)113993969A/B/CV297M

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (5, 15)

Asymmetric Unit (5, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003689841aENSE00001448527chr10:124221041-124221640600HTRA1_HUMAN1-1581580--
1.2ENST000003689842ENSE00001727698chr10:124248418-124248517100HTRA1_HUMAN158-191343A:161-191
B:161-190
C:164-191
31
30
28
1.3ENST000003689843ENSE00001656483chr10:124248938-124249142205HTRA1_HUMAN191-259693A:191-259
B:199-259
C:191-259 (gaps)
69
61
69
1.4ENST000003689844ENSE00001691312chr10:124266207-124266401195HTRA1_HUMAN260-324653A:260-324 (gaps)
B:260-324 (gaps)
C:260-324 (gaps)
65
65
65
1.5ENST000003689845ENSE00001099158chr10:124266886-12426691833HTRA1_HUMAN325-335113A:325-335
B:325-335
C:325-335
11
11
11
1.6ENST000003689846ENSE00001099160chr10:124268172-124268286115HTRA1_HUMAN336-374393A:336-364
B:336-364
C:336-364
29
29
29
1.7ENST000003689847ENSE00001099153chr10:124269612-12426966958HTRA1_HUMAN374-393200--
1.8ENST000003689848ENSE00001099157chr10:124271486-12427158196HTRA1_HUMAN393-425330--
1.9bENST000003689849bENSE00001608082chr10:124273707-124274424718HTRA1_HUMAN425-480560--

(-) Sequences/Alignments

Asymmetric 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:190
 aligned with HTRA1_HUMAN | Q92743 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:204
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360    
          HTRA1_HUMAN   161 DPNSLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGKELGLRNSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFL 364
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..eeeeeeeee......eeeeeeeeeeeee...eeee.........eeeee.....eeeeeeeeee....eeeee.............hhhhh....eeeeee.......eeeeeeeee.--------------..eee...........eeee....eeeeeeeeee..eeeeeehhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -----L------P------------------------------------------------------------------------------T-------------------------------GQV----------M------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------R-------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:161-191       --------------------------------------------------------------------Exon 1.4  PDB: A:260-324 (gaps) UniProt: 260-324                 Exon 1.5   Exon 1.6  PDB: A:336-364      Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: A:191-259 UniProt: 191-259                            --------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3nwu A 161 DPNSLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTT--------------DYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFL 364
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300         -    |  320       330       340       350       360    
                                                                                                                                                                     300            315                                                 

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with HTRA1_HUMAN | Q92743 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:204
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360    
          HTRA1_HUMAN   161 DPNSLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGKELGLRNSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFL 364
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh..eeeeeee.--------...eeeeeeeee...eeee.........eeeee.....eeeeeeeeee....eeeee.............hhhhh....eeeeee.......eeeeeeeee.-------------...eee...........eeee....eeeeeeeeee..eeeeeehhhhhhh. Sec.struct. author
             SAPs(SNPs) (1) -----L------P------------------------------------------------------------------------------T-------------------------------GQV----------M------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------R-------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:161-190       --------------------------------------------------------------------Exon 1.4  PDB: B:260-324 (gaps) UniProt: 260-324                 Exon 1.5   Exon 1.6  PDB: B:336-364      Transcript 1 (1)
           Transcript 1 (2) ------------------------------Exon 1.3  PDB: B:199-259 UniProt: 191-259 [INCOMPLETE]               --------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3nwu B 161 DPNSLRHKYNFIADVVEKIAPAVVHIELFR--------VPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTT-------------MDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFL 364
                                   170       180       190       200       210       220       230       240       250       260       270       280       290       300         -   |   320       330       340       350       360    
                                                       190      199                                                                                                  300           314                                                  

Chain C from PDB  Type:PROTEIN  Length:183
 aligned with HTRA1_HUMAN | Q92743 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:201
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363 
          HTRA1_HUMAN   164 SLRHKYNFIADVVEKIAPAVVHIELFRKLPFSKREVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTTQRGGKELGLRNSDMDYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFL 364
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------    ------Trypsin_2-3nwuC01 C:204-342                                                                                                                ---------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------    ------Trypsin_2-3nwuC02 C:204-342                                                                                                                ---------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------    ------Trypsin_2-3nwuC03 C:204-342                                                                                                                ---------------------- Pfam domains (3)
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeeeeeee...----.eeeeeeeeeeee...eeee.........eeeee.....eeeeeeeeee....eeeee.............hhhhh....eeeeee.......eeeeeeeee.--------------..eee...........eee.....eeeeeeeeee..eeeeeehhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) --L------P------------------------------------------------------------------------------T-------------------------------GQV----------M------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------R-------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: C:164-191    --------------------------------------------------------------------Exon 1.4  PDB: C:260-324 (gaps) UniProt: 260-324                 Exon 1.5   Exon 1.6  PDB: C:336-364      Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.3  PDB: C:191-259 (gaps) UniProt: 191-259                     --------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3nwu C 164 SLRHKYNFIADVVEKIAPAVVHIELFRKLP----EVPVASGSGFIVSEDGLIVTNAHVVTNKHRVKVELKNGATYEAKIKDVDEKADIALIKIDHQGKLPVLLLGRSSELRPGEFVVAIGSPFSLQNTVTTGIVSTT--------------DYIQTDAIINYGNSGGPLVNLDGEVIGINTLKVTAGISFAIPSDKIKKFL 364
                                   173       183       193    |  203       213       223       233       243       253       263       273       283       293      |  -         - |     323       333       343       353       363 
                                                       193  198                                                                                                   300            315                                                 

   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 3NWU)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NWU)

(-) Pfam Domains  (1, 3)

Asymmetric Unit

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (HTRA1_HUMAN | Q92743)
molecular function
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    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:0005520    insulin-like growth factor binding    Interacting selectively and non-covalently with an insulin-like growth factor, any member of a group of polypeptides that are structurally homologous to insulin and share many of its biological activities, but are immunologically distinct from it.
    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: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: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:0060718    chorionic trophoblast cell differentiation    The process in which relatively unspecialized cells of the ectoplacental cone acquire specialized structural and/or functional features that characterize chorionic trophoblasts. These cells will migrate towards the spongiotrophoblast layer and give rise to syncytiotrophoblasts of the labyrinthine layer.
    GO:0097187    dentinogenesis    The process whose specific outcome is the formation of dentin, the mineralized tissue that constitutes the major bulk of teeth. Dentin may be one of three types: primary dentin, secondary dentin, and tertiary dentin.
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    GO:0030514    negative regulation of BMP signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway.
    GO:0050687    negative regulation of defense response to virus    Any process that stops, prevents or reduces the rate or extent of antiviral mechanisms, thereby facilitating viral replication.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0001890    placenta development    The process whose specific outcome is the progression of the placenta over time, from its formation to the mature structure. The placenta is an organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin.
    GO:0050679    positive regulation of epithelial cell proliferation    Any process that activates or increases the rate or extent of epithelial cell proliferation.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0001558    regulation of cell growth    Any process that modulates the frequency, rate, extent or direction of cell growth.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
        HTRA1_HUMAN | Q927432joa 2ytw 3num 3nzi 3tjn 3tjo 3tjq

(-) Related Entries Specified in the PDB File

3num