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(-) Description

Title :  CRYSTAL STRUCTURE OF ACTIVE GRANZYME M BOUND TO ITS PRODUCT
 
Authors :  L. F. Wu, L. Wang, G. Q. Hua, K. Liu, Y. J. Zhai, F. Sun, Z. S. Fan
Date :  22 Jan 08  (Deposition) - 27 Jan 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine Protease, Synthesized Peptide, Cytolysis, Glycoprotein, Hydrolase, Protease, Secreted, Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Wu, L. Wang, G. Hua, K. Liu, X. Yang, Y. Zhai, M. Bartlam, F. Sun, Z. Fan
Structural Basis For Proteolytic Specificity Of The Human Apoptosis-Inducing Granzyme M
J. Immunol. V. 183 421 2009
PubMed-ID: 19542453  |  Reference-DOI: 10.4049/JIMMUNOL.0803088

(-) Compounds

Molecule 1 - GRANZYME M
    ChainsA
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B-GZMM
    Expression System StrainROSETTA(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGZMM, MET1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMET-ASE, NATURAL KILLER CELL GRANULAR PROTEASE, HU-MET-1, MET-1 SERINE PROTEASE
 
Molecule 2 - SSGKVPL
    ChainsB
    EngineeredYES
    Other DetailsPEPTIDE SYNTHESIS
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:128 , SER A:135 , ARG A:136 , VAL A:137 , ARG A:139BINDING SITE FOR RESIDUE SO4 A 241
2AC2SOFTWAREGLN A:45 , ARG A:46 , MET A:47 , ALA A:48 , LYS A:173 , HOH A:296BINDING SITE FOR RESIDUE SO4 A 242
3AC3SOFTWAREARG A:51 , HIS A:67 , HOH A:359BINDING SITE FOR RESIDUE SO4 A 243
4AC4SOFTWARELYS A:34 , GLN A:91 , ARG A:203 , HOH A:375 , HOH A:409BINDING SITE FOR RESIDUE SO4 A 244
5AC5SOFTWAREGLY A:189 , LYS A:190 , HOH A:397BINDING SITE FOR RESIDUE SO4 A 245

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:42
2A:120 -A:188
3A:151 -A:167
4A:178 -A:205

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:80 -Pro A:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051829R221GGRAM_HUMANPolymorphism1599882AG196G

  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.GRAM_HUMAN26-254  1A:1-229
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAM_HUMAN62-67  1A:37-42
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAM_HUMAN201-212  1A:176-187

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002645531ENSE00001323868chr19:544027-544126100GRAM_HUMAN1-19190--
1.2ENST000002645532ENSE00001372154chr19:547280-547436157GRAM_HUMAN19-71531A:1-4646
1.3ENST000002645533ENSE00000655682chr19:548542-548677136GRAM_HUMAN71-116461A:46-9146
1.4ENST000002645534ENSE00000655684chr19:548922-549185264GRAM_HUMAN117-204881A:92-17988
1.5ENST000002645535ENSE00001054785chr19:549630-549919290GRAM_HUMAN205-257531A:180-23152

(-) 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:231
 aligned with GRAM_HUMAN | P51124 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:231
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 
           GRAM_HUMAN    26 IIGGREVIPHSRPYMASLQRNGSHLCGGVLVHPKWVLTAAHCLAQRMAQLRLVLGLHTLDSPGLTFHIKAAIQHPRYKPVPALENDLALLQLDGKVKPSRTIRPLALPSKRQVVAAGTRCSMAGWGLTHQGGRLSRVLRELDLQVLDTRMCNNSRFWNGSLSPSMVCLAADSKDQAPCKGDSGGPLVCGKGRVLARVLSFSSRVCTDIFKPPVATAVAPYVSWIRKVTGRS 256
               SCOP domains d2zgha_ A: automated matches                                                                                                                                                                                                            SCOP domains
               CATH domains 2zghA01     2zghA02 A:13-104,A:219-231 Trypsin-like serine proteases                                    2zghA01 A:1-12,A:105-218 Trypsin-like serine proteases                                                            2zghA02       CATH domains
               Pfam domains Trypsin-2zghA01 A:1-224                                                                                                                                                                                                         ------- Pfam domains
         Sec.struct. author ....ee........eeeeee..eeeeeeeeee..eeeehhhhhh.hhh.eeeee.........eee.eeeeee..............eeeee..........................eeeeee..............eeeeeeeehhhhhh............eeeee...............eeee....eeeeeeeee...........eeee...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G----------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:1-229 UniProt: 26-254                                                                                                                                                                                            -- PROSITE (1)
                PROSITE (2) ------------------------------------TRYPSI-------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:1-46 UniProt: 19-71          ---------------------------------------------Exon 1.4  PDB: A:92-179 UniProt: 117-204                                                Exon 1.5  PDB: A:180-231 UniProt: 205-257            Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------Exon 1.3  PDB: A:46-91 UniProt: 71-116        -------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2zgh A   1 IIGGREVIPHSRPYMASLQRNGSHLCGGVLVHPKWVLTAAHCLAQRMAQLRLVLGLHTLDSPGLTFHIKAAIQHPRYKPVPALENDLALLQLDGKVKPSRTIRPLALPSKRQVVAAGTRCSMAGWGLTHQGGRLSRVLRELDLQVLDTRMCNNSRFWNGSLSPSMVCLAADSKDQAPCKGDSGGPLVCGKGRVLAGVLSFSSRVCTDIFKPPVATAVAPYVSWIRKVTGRS 231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 

Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...ee. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 2zgh B   2 SGKVPL   7

   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/Biological Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GRAM_HUMAN | P51124)
molecular function
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    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: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:0008219    cell death    Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
    GO:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    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.
    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
        GRAM_HUMAN | P511241lzp 2zgc 2zgj 2zks

(-) Related Entries Specified in the PDB File

2zgc CRYSTAL STRUCTURE OF ACTIVE HUMAN GRANZYME M
2zgj CRYSTAL STRUCTURE OF D86N-GZMM COMPLEXED WITH ITS OPTIMAL SYNTHESIZED SUBSTRATE