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(-) Description

Title :  CRYSTAL STRUCTURE OF DESC1, A NEW MEMBER OF THE TYPE II TRANSMEMBRANE SERINE PROTEINASES FAMILY
 
Authors :  O. J. P. Kyrieleis, R. Huber, E. L. Madison, Jacob U.
Date :  31 Jan 07  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.61
Chains :  Asym./Biol. Unit :  A
Keywords :  Type Ii Trans-Membrane Serine Proteinases, Trypsin-Like Serine Protease, Tumor Marker, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  O. J. P. Kyrieleis, R. Huber, E. Ong, R. Oehler, M. Hunter, E. L. Madison, U. Jacob
Crystal Structure Of The Catalytic Domain Of Desc1, A New Member Of The Type Ii Transmembrane Serine Proteinase Family.
Febs J. V. 274 2148 2007
PubMed-ID: 17388811  |  Reference-DOI: 10.1111/J.1742-4658.2007.05756.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRANSMEMBRANE PROTEASE, SERINE 11E
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9K
    Expression System StrainSMD 1168
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GeneTMPRSS11E, DESC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERINE PROTEASE DESC1, TRANSMEMBRANE PROTEASE, SERINE 11E CATALYTIC CHAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:189 , ALA A:190 , GLN A:192 , SER A:195 , TRP A:215 , GLU A:218 , GLY A:226 , HOH A:254BINDING SITE FOR RESIDUE BEN A 245

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:168 -A:182
3A:191 -A:219

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1His A:96 -Pro A:97

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051847Y303CTM11E_HUMANPolymorphism976002AY128C

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.TM11E_HUMAN192-422  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.TM11E_HUMAN228-233  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.TM11E_HUMAN367-378  1A:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003053631ENSE00001596784chr4:69313167-6931324175TM11E_HUMAN1-440--
1.2ENST000003053632ENSE00001789388chr4:69327539-69327663125TM11E_HUMAN4-46430--
1.3ENST000003053633ENSE00001784863chr4:69332349-69332470122TM11E_HUMAN46-86410--
1.4ENST000003053634ENSE00001740194chr4:69334597-6933466468TM11E_HUMAN87-109230--
1.5ENST000003053635ENSE00001690619chr4:69337178-69337341164TM11E_HUMAN109-164560--
1.6ENST000003053636ENSE00001697113chr4:69340441-6934047939TM11E_HUMAN164-177140--
1.7ENST000003053637ENSE00001738512chr4:69341979-69342156178TM11E_HUMAN177-236601A:16-62 (gaps)47
1.8aENST000003053638aENSE00001714583chr4:69343087-69343346260TM11E_HUMAN236-323881A:62-148 (gaps)93
1.9ENST000003053639ENSE00001660015chr4:69344567-69344709143TM11E_HUMAN323-370481A:148-192 (gaps)49
1.10ENST0000030536310ENSE00001760089chr4:69362361-69363322962TM11E_HUMAN371-423531A:193-24453

(-) 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:232
 aligned with TM11E_HUMAN | Q9UL52 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:232
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421  
         TM11E_HUMAN    192 IVGGTEVEEGEWPWQASLQWDGSHRCGATLINATWLVSAAHCFTTYKNPARWTASFGVTIKPSKMKRGLRRIIVHEKYKHPSHDYDISLAELSSPVPYTNAVHRVCLPDASYEFQPGDVMFVTGFGALKNDGYSQNHLRQAQVTLIDATTCNEPQAYNDAITPRMLCAGSLEGKTDACQGDSGGPLVSSDARDIWYLAGIVSWGDECAKPNKPGVYTRVTALRDWITSKTGI  423
               SCOP domains d2oq5a_ A: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains 2oq5A01     2oq5A02 A:28-120,A:233-244 Trypsin-like serine proteases                                    2oq5A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                             2oq5A02      CATH domains
               Pfam domains Trypsin-2oq5A01 A:16-238                                                                                                                                                                                                          ------ Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh...hhh.eeeee........eeeeeeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh............eeeee...............eeeee.....eeeeeeeee..........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 192-422                                                                                                                                                                                            - PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7  PDB: A:16-62 (gaps) [INCOMPLETE]   --------------------------------------------------------------------------------------Exon 1.9  PDB: A:148-192 (gaps) UniProt: 323-370Exon 1.10  PDB: A:193-244 UniProt: 371-423            Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------Exon 1.8a  PDB: A:62-148 (gaps) UniProt: 236-323                                        ---------------------------------------------------------------------------------------------------- Transcript 1 (2)
                2oq5 A   16 IVGGTEVEEGEWPWQASLQWDGSHRCGATLINATWLVSAAHCFTTYKNPARWTASFGVTIKPSKMKRGLRRIIVHEKYKHPSHDYDISLAELSSPVPYTNAVHRVCLPDASYEFQPGDVMFVTGFGALKNDGYSQNHLRQAQVTLIDATTCNEPQAYNDAITPRMLCAGSLEGKTDACQGDSGGPLVSSDARDIWYLAGIVSWGDECAKPNKPGVYTRVTALRDWITSKTGI  244
                                    25        36        46        56 ||    64C||     |75       |86        96       106       116       126       136       146  ||   157       167   ||  175      184A|      193       203  |    212       222       232       242  
                                             34|                    58|  64A||||   69A|       83|                                                             149|                170A|           184A|                  205A                                       
                                              36                     60   64B|||     74        85                                                              151                 170B            184B                                                             
                                                                           64C||                                                                                                                                                                                    
                                                                            64D|                                                                                                                                                                                    
                                                                             64E                                                                                                                                                                                    

   Legend:   → Mismatch (orange background)
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  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  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TM11E_HUMAN | Q9UL52)
molecular function
    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: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:0050890    cognition    The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    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: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: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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