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(-) Description

Title :  CATALYTIC DOMAIN OF VAMPIRE BAT (DESMODUS ROTUNDUS) SALIVA PLASMINOGEN ACTIVATOR IN COMPLEX WITH EGR-CMK (GLU-GLY-ARG CHLOROMETHYL KETONE)
 
Authors :  M. Renatus, M. T. Stubbs, W. Bode
Date :  17 Feb 98  (Deposition) - 23 Mar 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease, Fibrinolytic Enzymes, Plasminogen Activators, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Renatus, M. T. Stubbs, R. Huber, P. Bringmann, P. Donner, W. D. Schleuning, W. Bode
Catalytic Domain Structure Of Vampire Bat Plasminogen Activator: A Molecular Paradigm For Proteolysis Without Activation Cleavage.
Biochemistry V. 36 13483 1997
PubMed-ID: 9354616  |  Reference-DOI: 10.1021/BI971129X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMINOGEN ACTIVATOR
    Chains: A
    EC Number: 3.4.21.68
    Engineered: YES
    Expression System: MESOCRICETUS AURATUS
    Expression System Cell Line: BHK
    Expression System Common: GOLDEN HAMSTER
    Expression System Taxid: 10036
    Fragment: UNP RESIDUES 213-477
    Organ: SALIVARY GLANDS
    Organism Common: COMMON VAMPIRE BAT
    Organism Scientific: DESMODUS ROTUNDUS
    Organism Taxid: 9430

 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
10GJ1Ligand/IonL-ALPHA-GLUTAMYL-N-{(1S)-4-{[AMINO(IMINIO)METHYL]AMINO}-1-[(1S)-2-CHLORO-1-HYDROXYETHYL]BUTYL}GLYCINAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:57 , TYR A:99 , LYS A:174 , ASP A:189 , ALA A:190 , CYS A:191 , GLN A:192 , GLY A:193 , ASP A:194 , SER A:195 , SER A:214 , TRP A:215 , GLY A:216 , GLY A:219BINDING SITE FOR RESIDUE 0GJ A 245

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:1 -A:122
2A:42 -A:58
3A:50 -A:111
4A:136 -A:201
5A:168 -A:182
6A:191 -A:220

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A5I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A5I)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.URT1_DESRO226-476  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.URT1_DESRO268-273  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.URT1_DESRO422-433  1A:189-200

(-) Exons   (0, 0)

(no "Exon" information available for 1A5I)

(-) 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:265
 aligned with URT1_DESRO | P98119 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:265
                                   222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472     
          URT1_DESRO    213 TCGLRKYKEPQLHSTGGLFTDITSHPWQAAIFAQNRRSSGERFLCGGILISSCWVLTAAHCFQESYLPDQLKVVLGRTYRVKPGEEEQTFKVKKYIVHKEFDDDTYNNDIALLQLKSDSPQCAQESDSVRAICLPEANLQLPDWTECELSGYGKHKSSSPFYSEQLKEGHVRLYPSSRCAPKFLFNKTVTNNMLCAGDTRSGEIYPNVHDACQGDSGGPLVCMNDNHMTLLGIISWGVGCGEKDVPGVYTKVTNYLGWIRDNMHL  477
               SCOP domains d1a5ia_ A: Single chain tissue plasminogen activator                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------1a5iA01     1a5iA02 A:28-120,A:233-244 Trypsin-like serine proteases                                                  1a5iA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                                   1a5iA02      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhh..eeeeee........eeeeeeeeee..eeee.hhh..........eeee............eeeeeeeeee.............eeeeee.............................eeeeee...............eeeeee...hhh..............eeee......................eeeeee..eeeeeeeeee..........eeeeehhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------TRYPSIN_DOM  PDB: A:16-243 UniProt: 226-476                                                                                                                                                                                                                - PROSITE (1)
                PROSITE (2) -------------------------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1a5i A   1A TCGLRKYKEPQLHSTGGLFTDITSHPWQAAIFAQNRRSSGERFLCGGILISSCWVLTAAHCFQESYLPDQLKVVLGRTYRVKPGEEEQTFKVKKYIVHKEFDDDTYNNDIALLQLKSDSPQCAQESDSVRAICLPEANLQLPDWTECELSGYGKHKSSSPFYSEQLKEGHVRLYPSSRCAPKFLFNKTVTNNMLCAGDTRSGEIYPNVHDACQGDSGGPLVCMNDNHMTLLGIISWGVGCGEKDVPGVYTKVTNYLGWIRDNMHL  244
                            |        9  ||    22        32     ||37E        47        57   |||| 63        73        83        93       103      110C|      119       129       139       149       159       169||     177      186A|||||||189       199       209       220 |     229       239     
                            |          12|                   37A||||                     60A|||                                               110A|||                                                        169A|              186A|||||||                            217|  |                       
                           1A           16                    37B|||                      60B||                                                110B||                                                         169B               186B||||||                             219  |                       
                                                               37C||                       60C|                                                 110C|                                                                             186C|||||                               221A                       
                                                                37D|                        60D                                                  110D                                                                              186D||||                                                          
                                                                 37E                                                                                                                                                                186E|||                                                          
                                                                                                                                                                                                                                     186F||                                                          
                                                                                                                                                                                                                                      186G|                                                          
                                                                                                                                                                                                                                       186H
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A5I)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (URT1_DESRO | P98119)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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.
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.

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