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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GRANZYME H
 
Authors :  L. Wang, K. Zhang, L. Wu, L. Tong, F. Sun, Z. Fan
Date :  25 Aug 11  (Deposition) - 28 Dec 11  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Serine Protease, Hydrolase, Cytolysis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Wang, K. Zhang, L. Wu, S. Liu, H. Zhang, Q. Zhou, L. Tong, F. Sun, Z. Fan
Structural Insights Into The Substrate Specificity Of Human Granzyme H: The Functional Roles Of A Novel Rkr Motif
J. Immunol. V. 188 765 2012
PubMed-ID: 22156497  |  Reference-DOI: 10.4049/JIMMUNOL.1101381

(-) Compounds

Molecule 1 - GRANZYME H
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-28A
    Expression System StrainROSSETA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGZMH, CGL2, CTSGL2
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGZMH, CCP-X, CATHEPSIN G-LIKE 2, CTSGL2, CYTOTOXIC T- LYMPHOCYTE PROTEINASE, CYTOTOXIC SERINE PROTEASE C, CSP-C

 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
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:41 , ARG A:43 , LYS A:75BINDING SITE FOR RESIDUE SO4 A 300

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:44 -A:60
2A:137 -A:203
3A:167 -A:182

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:220 -Pro A:221

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014556R84QGRAH_HUMANPolymorphism20545AR79Q

  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.GRAH_HUMAN21-244  1A:16-239
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAH_HUMAN60-65  1A:55-60
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAH_HUMAN196-207  1A:191-202

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002163381ENSE00000889483chr14:25078864-25078765100GRAH_HUMAN1-19190--
1.2aENST000002163382aENSE00000654537chr14:25077618-25077471148GRAH_HUMAN19-68501A:16-6348
1.3ENST000002163383ENSE00001596918chr14:25076953-25076818136GRAH_HUMAN68-113461A:63-10846
1.4ENST000002163384ENSE00000654535chr14:25076612-25076355258GRAH_HUMAN114-199861A:109-19486
1.5bENST000002163385bENSE00001918960chr14:25075952-25075688265GRAH_HUMAN200-246471A:195-24147

(-) 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:226
 aligned with GRAH_HUMAN | P20718 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:226
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
           GRAH_HUMAN    21 IIGGHEAKPHSRPYMAFVQFLQEKSRKRCGGILVRKDFVLTAAHCQGSSINVTLGAHNIKEQERTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKWTTAVRPLRLPSSKAQVKPGQLCSVAGWGYVSMSTLATTLQEVLLTVQKDCQCERLFHGNYSRATEICVGDPKKTQTGFKGDSGGPLVCKDVAQGILSYGNKKGTPPGVYIKVSHFLPWIKRTMKRL 246
               SCOP domains d3tk9a_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee....eeeeeeeeee..eeee......eeeeeee............eeeeeeeeee.............eeeee..........................eeeeee.............eeeeeeeehhhhhhhhh........eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-239 UniProt: 21-244                                                                                                                                                                                      -- PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER --------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2a  PDB: A:16-63 UniProt: 19-68          ---------------------------------------------Exon 1.4  PDB: A:109-194 UniProt: 114-199                                             Exon 1.5b  PDB: A:195-241 UniProt: 200-246      Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3  PDB: A:63-108 UniProt: 68-113       ------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3tk9 A  16 IIGGHEAKPHSRPYMAFVQFLQEKSRKRCGGILVRKDFVLTAAHCQGSSINVTLGAHNIKEQERTQQFIPVKRPIPHPAYNPKNFSNNIMLLQLERKAKWTTAVRPLRLPSSKAQVKPGQLCSVAGWGYVSMSTLATTLQEVLLTVQKDCQCERLFHGNYSRATEICVGDPKKTQTGFKGDSGGPLVCKDVAQGILSYGNKKGTPPGVYIKVSHFLPWIKRTMKRL 241
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235      

   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  (0, 0)

(no "CATH Domain" information available for 3TK9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TK9)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GRAH_HUMAN | P20718)
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: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:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRAH_HUMAN | P207181lxv 3tju 3tjv 4gaw

(-) Related Entries Specified in the PDB File

3tju 3tjv