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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PRO-GRANZYME K
 
Authors :  C. Hink-Schauer, E. Estebanez-Perpina, E. Wilharm, P. Fuentes- Prior, W. Klinkert, W. Bode, D. E. Jenne
Date :  07 Oct 02  (Deposition) - 14 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Granzyme, Apoptosis, Serine Protease, S1 Family, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Hink-Schauer, E. Estebanez-Perpina, E. Wilharm, P. Fuentes-Prior, W. Klinkert, W. Bode, D. E. Jenne
The 2. 2-A Crystal Structure Of Human Pro-Granzyme K Reveals A Rigid Zymogen With Unusual Features
J. Biol. Chem. V. 277 50923 2002
PubMed-ID: 12384499  |  Reference-DOI: 10.1074/JBC.M207962200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PRO-GRANZYME K
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24C+
    Expression System StrainB834 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGRANZYME K, GRANZYME 3, NK-TRYPTASE-2
    TissueBONE MARROW

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1MZD)

(-) Sites  (0, 0)

(no "Site" information available for 1MZD)

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asp A:173B-Pro A:174
2Val A:243 -Pro A:244

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAK_HUMAN27-259  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAK_HUMAN63-68  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAK_HUMAN208-219  1A:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002310091ENSE00000815160chr5:54320081-54320214134GRAK_HUMAN1-22220--
1.2ENST000002310092ENSE00000743501chr5:54320488-54320635148GRAK_HUMAN22-71501A:14-60A (gaps)48
1.3bENST000002310093bENSE00000743506chr5:54326262-54326412151GRAK_HUMAN71-121511A:60A-10751
1.4bENST000002310094bENSE00000743511chr5:54327192-54327461270GRAK_HUMAN122-211901A:108-192 (gaps)92
1.5ENST000002310095ENSE00000815161chr5:54329593-54330398806GRAK_HUMAN212-264531A:193-248 (gaps)58

(-) 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:240
 aligned with GRAK_HUMAN | P49863 from UniProtKB/Swiss-Prot  Length:264

    Alignment length:240
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264
          GRAK_HUMAN     25 MEIIGGKEVSPHSRPFMASIQYGGHHVCGGVLIDPQWVLTAAHCQYRFTKGQSPTVVLGAHSLSKNEASKQTLEIKKFIPFSRVTSDPQSNDIMLVKLQTAAKLNKHVKMLHIRSKTSLRSGTKCKVTGWGATDPDSLRPSDTLREVTVTVLSRKLCNSQSYYNGDPFITKDMVCAGDAKGQKDSCKGDSGGPLICKGVFHAIVSGGHECGVATKPGIYTLLTKKYQTWIKSNLVPPHTN  264
               SCOP domains d1mzda_ A: Granzyme K                                                                                                                                                                                                                            SCOP domains
               CATH domains --1mzdA01     1mzdA02 A:28-120,A:233-245 Trypsin-like serine proteases                                        1mzdA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                          -1mzdA02      --- CATH domains
               Pfam domains --Trypsin-1mzdA01 A:16-238                                                                                                                                                                                                            ---------- Pfam domains
         Sec.struct. author ......ee..........eeee..eeee..eeee..eeee.............eeeee............eeeeeeeeee.............eeeee.........................eeeeee...............eeeeeee.hhhhhh..............eeeee...............eeee..eeeeee............eeeee.hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --TRYPSIN_DOM  PDB: A:16-243 UniProt: 27-259                                                                                                                                                                                               ----- PROSITE (1)
                PROSITE (2) --------------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:14-60A (gaps) UniProt: 22-71  --------------------------------------------------Exon 1.4b  PDB: A:108-192 (gaps) UniProt: 122-211                                         Exon 1.5  PDB: A:193-248 (gaps) UniProt: 212-264      Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------Exon 1.3b  PDB: A:60A-107 UniProt: 71-121          ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1mzd A   14 MEIIGGKEVSPHSRPFMASIQYGGHHVCGGVLIDPQWVLTAAHCQYRFTKGQSPTVVLGAHSLSKNEASKQTLEIKKFIPFSRVTSDPQSNDIMLVKLQTAAKLNKHVKMLHIRSKTSLRSGTKCKVTGWGATDPDSLRPSDTLREVTVTVLSRKLCNSQSYYNGDPFITKDMVCAGDAKGQKDSCKGDAGGPLICKGVFHAIVSGGHECGVATKPGIYTLLTKKYQTWIKSNLVPPHTN  248
                                    23        33 ||     44        54      |60D        70        80        90       100       110       120     ||131       141       151       161      170A|   || 177       187 ||    195      |209       220   |   229   |   238       248
                                                35|                     60A|||                                                               126|                 148A||                170A|   ||            188A|           202||      217| 223A      232A                
                                                 37                      60B||                                                                128                   149|                 170B   ||             188B            205|       219                               
                                                                          60C|                                                                                       151                     173A|                              208                                         
                                                                           60D                                                                                                                173B                                                                          

   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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GRAK_HUMAN | P49863)
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.
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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  Sites
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  Cis Peptide Bonds
    Asp A:173B - Pro A:174   [ RasMol ]  
    Val A:243 - Pro A:244   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRAK_HUMAN | P498631mza

(-) Related Entries Specified in the PDB File

1mza 1MZA CONTAINS GRANZYME K AT 2.23A