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(-) Description

Title :  THE OLIGOMERIC STRUCTURE OF HUMAN GRANZYME A REVEALS THE MOLECULAR DETERMINANTS OF SUBSTRATE SPECIFICITY
 
Authors :  J. K. Bell, D. H. Goetz, S. Mahrus, J. L. Harris, R. J. Fletterick, C. S. Cr
Date :  12 Mar 03  (Deposition) - 01 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. K. Bell, D. H. Goetz, S. Mahrus, J. L. Harris, R. J. Fletterick, C. S. Craik
The Oligomeric Structure Of Human Granzyme A Is A Determinant Of Its Extended Substrate Specificity.
Nat. Struct. Biol. V. 10 527 2003
PubMed-ID: 12819769  |  Reference-DOI: 10.1038/NSB944

(-) Compounds

Molecule 1 - GRANZYME A
    ChainsA
    EC Number3.4.21.78
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPICZALPHAA
    Expression System StrainX33
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    GeneGZMA
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYTOTOXIC T-LYMPHOCYTE PROTEINASE 1, HANUKKAH FACTOR, H FACTOR, HF, GRANZYME 1, CTL TRYPTASE, FRAGMENTIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
10G61Ligand/IonD-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
10G62Ligand/IonD-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:57 , ASP A:189 , SER A:190 , CYS A:191 , GLY A:193 , SER A:195 , SER A:214 , PHE A:215 , GLY A:216 , GLU A:218 , GLY A:226 , HOH A:272 , HOH A:372 , HOH A:373 , HOH A:374 , HOH A:375BINDING SITE FOR RESIDUE 0G6 A 1
2AC2SOFTWARESER A:184B , LEU A:185 , ARG A:186 , ARG A:188B , HOH A:306BINDING SITE FOR RESIDUE SO4 A 247

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:42 -A:58
2A:93 -A:93
3A:136 -A:201
4A:168 -A:182
5A:191 -A:220

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:175A-Pro A:175B

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024291M121TGRAA_HUMANPolymorphism3104233AT109T

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_024291M121TGRAA_HUMANPolymorphism3104233AT109T

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

(-) PROSITE Motifs  (3, 3)

Asymmetric Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAA_HUMAN29-259  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAA_HUMAN65-70  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAA_HUMAN206-217  1A:189-200
Biological Unit 1 (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.GRAA_HUMAN29-259  2A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAA_HUMAN65-70  2A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAA_HUMAN206-217  2A:189-200

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002743061ENSE00001127870chr5:54398476-54398580105GRAA_HUMAN1-24240--
1.2ENST000002743062ENSE00000971463chr5:54401302-54401446145GRAA_HUMAN24-72491A:16-60 (gaps)45
1.3ENST000002743063ENSE00000971464chr5:54403622-54403763142GRAA_HUMAN72-119481A:60-107 (gaps)49
1.4ENST000002743064ENSE00000971465chr5:54403953-54404222270GRAA_HUMAN120-209901A:108-192 (gaps)91
1.5ENST000002743065ENSE00001127864chr5:54405849-54406080232GRAA_HUMAN210-262531A:193-244 (gaps)55

(-) 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:232
 aligned with GRAA_HUMAN | P12544 from UniProtKB/Swiss-Prot  Length:262

    Alignment length:232
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258  
          GRAA_HUMAN     29 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLMEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVNITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKG  260
               SCOP domains d1orfa_ A: Granzyme A                                                                                                                                                                                                                    SCOP domains
               CATH domains 1orfA01     1orfA02 A:28-120,A:233A-244 Trypsin-like serine proteases                                   1orfA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                            1orfA02       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeee.....eeeeeeee..eeee..........eeee............eee.eeeeee.............eeeee..........................eeeeee..............eeeeeeeehhhhhh..............eeeee...............eeee..eeeeeeee............eeeee.hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------T------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 29-259                                                                                                                                                                                             - PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-60 (gaps) UniProt: 24-72-----------------------------------------------Exon 1.4  PDB: A:108-192 (gaps) UniProt: 120-209                                          Exon 1.5  PDB: A:193-244 (gaps) UniProt: 210-262    Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.3  PDB: A:60-107 (gaps) UniProt: 72-119  --------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1orf A   16 IIGGNEVTPHSRPYMVLLSLDRKTICAGALIAKDWVLTAAHCNLNKRSQVILGAHSITREEPTKQIMLVKKEFPYPCYDPATREGDLKLLQLTEKAKINKYVTILHLPKKGDDVKPGTMCQVAGWGRTHNSASWSDTLREVEITIIDRKVCNDRNHYNFNPVIGMNMVCAGSLRGGRDSCNGDSGSPLLCEGVFRGVTSFGLENKCGDPRGPGVYILLSKKHLNWIIMTIKG  244
                                    25        35    ||  46        56     || 66        76        86        96       106       116       126       136       146|      157       167  ||| 175A||     183||   ||191       201||     215   || |223      233A|      242  
                                                   40|                 62A| ||                                                                             146|                  170A|| 175A||     184A|   ||           202|        219A| ||        233A|           
                                                    42                  62B ||                                                                              148                   170B|  175B|      184B   ||            207         219B ||         233B           
                                                                           64|                                                                                                     170C   175C          188A|                          221A|                        
                                                                            66                                                                                                                           188B                           221B                        

   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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A   (GRAA_HUMAN | P12544)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0032078    negative regulation of endodeoxyribonuclease activity    Any process that stops or reduces the rate of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
    GO:0051354    negative regulation of oxidoreductase activity    Any process that stops or reduces the rate of oxidoreductase activity, the catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0051603    proteolysis involved in cellular protein catabolic process    The hydrolysis of a peptide bond or bonds within a protein as part of the chemical reactions and pathways resulting in the breakdown of a protein by individual cells.
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:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

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        GRAA_HUMAN | P125441hf1 1op8

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