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(-) Description

Title :  CRYSTAL STRUCTURE OF MT-SP1 IN COMPLEX WITH BENZAMIDINE
 
Authors :  C. Yuan, M. Huang, L. Chen
Date :  13 Oct 10  (Deposition) - 03 Aug 11  (Release) - 03 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Yuan, L. Chen, E. J. Meehan, N. Daly, D. J. Craik, M. Huang, J. C. Ngo
Structure Of Catalytic Domain Of Matriptase In Complex With Sunflower Trypsin Inhibitor-1.
Bmc Struct. Biol. V. 11 30 2011
PubMed-ID: 21693064  |  Reference-DOI: 10.1186/1472-6807-11-30

(-) Compounds

Molecule 1 - ST14 PROTEIN
    Chains: A
    EC Number: 3.4.21.109
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: YEAST
    Expression System Plasmid: PPICZALPHA
    Expression System Strain: X33
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP 182-422)
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MEMBRANE-TYPE SERINE PROTEASE 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3GSH1Ligand/IonGLUTATHIONE
4SO43Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:135 , ARG A:161 , HOH A:1084 , HOH A:1123 , HOH A:1142 , HOH A:1189 , HOH A:1296 , HOH A:1309BINDING SITE FOR RESIDUE SO4 A 1003
2AC2SOFTWARETHR A:62 , ARG A:84 , LEU A:85 , HOH A:1014 , HOH A:1191 , HOH A:1197 , HOH A:1222BINDING SITE FOR RESIDUE EDO A 1006
3AC3SOFTWAREPHE A:184A , LEU A:185 , SER A:186 , HOH A:1042 , HOH A:1224 , HOH A:1273 , HOH A:1274BINDING SITE FOR RESIDUE SO4 A 1004
4AC4SOFTWAREHIS A:57 , GLN A:192 , GLY A:193 , SER A:195 , BEN A:1002 , HOH A:1201 , HOH A:1205 , HOH A:1206 , HOH A:1215BINDING SITE FOR RESIDUE SO4 A 1005
5AC5SOFTWAREASP A:189 , SER A:190 , CYS A:191 , SER A:195 , VAL A:213 , TRP A:215 , GLY A:216 , GLY A:219 , CYS A:220 , GLY A:226 , SO4 A:1005 , HOH A:1183 , HOH A:1200 , HOH A:1213BINDING SITE FOR RESIDUE BEN A 1002
6AC6SOFTWARETRP A:29 , ARG A:119 , PRO A:120 , CYS A:122 , ARG A:206 , ILE A:207 , HOH A:1028 , HOH A:1110 , HOH A:1250 , HOH A:1287BINDING SITE FOR RESIDUE GSH A 1001
7AC7SOFTWAREVAL A:129 , PHE A:130 , MET A:181 , ALA A:210 , ARG A:230 , PRO A:232 , HOH A:1198 , HOH A:1291BINDING SITE FOR RESIDUE EDO A 1007
8AC8SOFTWAREVAL A:80 , GLN A:81 , GLU A:82 , ARG A:83BINDING SITE FOR RESIDUE EDO A 1008
9AC9SOFTWAREALA A:132 , GLN A:164 , GLN A:165 , HOH A:1040 , HOH A:1195BINDING SITE FOR RESIDUE EDO A 1009

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:168 -A:182
3A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P8G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_032849G827RST14_HUMANDisease (ARCI11)137852931AG216R
  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.ST14_HUMAN615-854  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.ST14_HUMAN652-657  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.ST14_HUMAN799-810  1A:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002787421aENSE00001334626chr11:130029457-130029955499ST14_HUMAN1-27270--
1.2ENST000002787422ENSE00000990418chr11:130058009-130058168160ST14_HUMAN28-81540--
1.3ENST000002787423ENSE00000990419chr11:130058425-130058552128ST14_HUMAN81-123430--
1.4ENST000002787424ENSE00000990421chr11:130058764-13005883471ST14_HUMAN124-147240--
1.5cENST000002787425cENSE00000990422chr11:130059634-130059791158ST14_HUMAN147-200540--
1.6bENST000002787426bENSE00000990423chr11:130060008-13006004336ST14_HUMAN200-212130--
1.7bENST000002787427bENSE00001278516chr11:130060349-130060589241ST14_HUMAN212-292810--
1.8ENST000002787428ENSE00000990429chr11:130064044-130064183140ST14_HUMAN292-339480--
1.9ENST000002787429ENSE00000990430chr11:130064535-13006463298ST14_HUMAN339-371330--
1.10bENST0000027874210bENSE00000990431chr11:130066234-130066343110ST14_HUMAN372-408370--
1.11bENST0000027874211bENSE00000990432chr11:130066465-130066595131ST14_HUMAN408-452450--
1.12ENST0000027874212ENSE00000990433chr11:130067736-130067840105ST14_HUMAN452-487360--
1.13ENST0000027874213ENSE00000990434chr11:130068203-130068313111ST14_HUMAN487-524380--
1.14ENST0000027874214ENSE00000990435chr11:130068403-130068516114ST14_HUMAN524-562390--
1.15ENST0000027874215ENSE00000990436chr11:130068842-130068964123ST14_HUMAN562-603420--
1.16ENST0000027874216ENSE00000990437chr11:130069846-130070032187ST14_HUMAN603-665631A:16-60F51
1.17ENST0000027874217ENSE00000990438chr11:130078305-130078579275ST14_HUMAN665-757931A:60F-14893
1.18ENST0000027874218ENSE00000990439chr11:130079337-130079473137ST14_HUMAN757-802461A:148-192 (gaps)47
1.19bENST0000027874219bENSE00000990440chr11:130079557-130080271715ST14_HUMAN803-855531A:193-244 (gaps)54

(-) 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:241
 aligned with Q8WVC1_HUMAN | Q8WVC1 from UniProtKB/TrEMBL  Length:422

    Alignment length:241
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421 
        Q8WVC1_HUMAN    182 VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPICLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV  422
               SCOP domains d3p8ga_ A: Matriptase MTSP1                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee...eeeeeeee....eeeehhhhhh........hhh.eeeee.............eee.eeeeee.............eeeee..........................eeeeee..............eeeeeee.hhhhhhhhh.......eeeee...............eeeee.....eeeeeeeee..........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3p8g A   16 VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPICLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVIQQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV  244
                                    25        35        45        55     ||60E||||    66        76 |      85        95       105       115       125       135       145  ||   156       166       176       185 |     194       204|      213   ||  223       233       243 
                                                                       60A||||||||               77A                                                                    148|                               184A  |               204A          217|  |                       
                                                                        60B|||||||                                                                                       150                                  186A                              219  |                       
                                                                         60C||||||                                                                                                                                                                221A                       
                                                                          60D|||||                                                                                                                                                                                           
                                                                           60E||||                                                                                                                                                                                           
                                                                            60F|||                                                                                                                                                                                           
                                                                             60G||                                                                                                                                                                                           
                                                                              60H|                                                                                                                                                                                           
                                                                               60I                                                                                                                                                                                           


Chain A from PDB  Type:PROTEIN  Length:241
 aligned with ST14_HUMAN | Q9Y5Y6 from UniProtKB/Swiss-Prot  Length:855

    Alignment length:241
                                   624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834       844       854 
          ST14_HUMAN    615 VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPICLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVINQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV  855
               SCOP domains d3p8ga_ A: Matriptase MTSP1                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeee...eeeeeeee....eeeehhhhhh........hhh.eeeee.............eee.eeeeee.............eeeee..........................eeeeee..............eeeeeee.hhhhhhhhh.......eeeee...............eeeee.....eeeeeeeee..........eeeee...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R---------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 615-854                                                                                                                                                                                                     - PROSITE (1)
                PROSITE (2) -------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.16  PDB: A:16-60F UniProt: 603-665          -------------------------------------------------------------------------------------------Exon 1.18  PDB: A:148-192 (gaps)              Exon 1.19b  PDB: A:193-244 (gaps) UniProt: 803-855    Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------Exon 1.17  PDB: A:60F-148 UniProt: 665-757                                                   -------------------------------------------------------------------------------------------------- Transcript 1 (2)
                3p8g A   16 VVGGTDADEGEWPWQVSLHALGQGHICGASLISPNWLVSAAHCYIDDRGFRYSDPTQWTAFLGLHDQSQRSAPGVQERRLKRIISHPFFNDFTFDYDIALLELEKPAEYSSMVRPICLPDASHVFPAGKAIWVTGWGHTQYGGTGALILQKGEIRVIQQTTCENLLPQQITPRMMCVGFLSGGVDSCQGDSGGPLSSVEADGRIFQAGVVSWGDGCAQRNKPGVYTRLPLFRDWIKENTGV  244
                                    25        35        45        55     ||60E||||    66        76 |      85        95       105       115       125       135       145  ||   156       166       176       185 |     194       204|      213   ||  223       233       243 
                                                                       60A||||||||               77A                                                                    148|                               184A  |               204A          217|  |                       
                                                                        60B|||||||                                                                                       150                                  186A                              219  |                       
                                                                         60C||||||                                                                                                                                                                221A                       
                                                                          60D|||||                                                                                                                                                                                           
                                                                           60E||||                                                                                                                                                                                           
                                                                            60F|||                                                                                                                                                                                           
                                                                             60G||                                                                                                                                                                                           
                                                                              60H|                                                                                                                                                                                           
                                                                               60I
   Legend:   → Mismatch (orange background)
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  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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P8G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P8G)

(-) Gene Ontology  (17, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ST14_HUMAN | Q9Y5Y6)
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:0060672    epithelial cell morphogenesis involved in placental branching    The change in form (cell shape and size) that occurs when a trophoblast cell elongates to contribute to the branching of the placenta.
    GO:0030216    keratinocyte differentiation    The process in which a relatively unspecialized cell acquires specialized features of a keratinocyte.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    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.
    GO:0019897    extrinsic component of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    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.

Chain A   (Q8WVC1_HUMAN | Q8WVC1)
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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8WVC1_HUMAN | Q8WVC1: 3p8f
        ST14_HUMAN | Q9Y5Y6: 1eaw 1eax 2fmv 2gv6 2gv7 3bn9 3ncl 3nps 3p8f 3so3 4is5 4isl 4isn 4iso 4jyt 4jz1 4jzi 4o97 4o9v 4r0i

(-) Related Entries Specified in the PDB File

3p8f