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(-) Description

Title :  HUMAN GRANZYME B IN COMPLEX WITH AC-IEPD-CHO
 
Authors :  J. Rotonda, M. Garcia-Calvo, H. G. Bull, W. M. Geissler, B. M. Mckeever, C. A. Willoughby, N. A. Thornberry, J. W. Becker
Date :  23 Mar 01  (Deposition) - 02 May 01  (Release) - 04 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Rotonda, M. Garcia-Calvo, H. G. Bull, W. M. Geissler, B. M. Mckeever C. A. Willoughby, N. A. Thornberry, J. W. Becker
The Three-Dimensional Structure Of Human Granzyme B Compare To Caspase-3, Key Mediators Of Cell Death With Cleavage Specificity For Aspartic Acid In P1.
Chem. Biol. V. 8 357 2001
PubMed-ID: 11325591  |  Reference-DOI: 10.1016/S1074-5521(01)00018-7

(-) Compounds

Molecule 1 - GRANZYME B
    Chains: A
    EC Number: 3.4.21.79
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - ACETYL-ISOLEUCYL-GLUTAMYL-PROLYL-ASPARTYL-ALDEHYDE PEPTIDE INHIBITOR
    Chains: B
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED.
    Synonym: ACE-ILE-GLU-PRO-ASP-CHO
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 14)

Asymmetric/Biological Unit (7, 14)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ASJ1Mod. Amino Acid(3S)-3-AMINO-4-HYDROXYBUTANOIC ACID
3BMA1Ligand/IonBETA-D-MANNOSE
4FUC1Ligand/IonALPHA-L-FUCOSE
5MAN1Ligand/IonALPHA-D-MANNOSE
6NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
7ZN5Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:34 , SER A:63 , ASN A:65BINDING SITE FOR RESIDUE NAG A 301
2AC2SOFTWAREARG A:48 , ASP A:50 , GLN A:107 , ARG A:166 , MET A:242 , ARG A:244 , MAN A:305BINDING SITE FOR RESIDUE BMA A 307
3AC3SOFTWAREHIS A:151 , HIS A:153BINDING SITE FOR RESIDUE ZN A 501
4AC4SOFTWAREHIS A:25 , GLU A:77 , HIS A:173 , HOH A:605BINDING SITE FOR RESIDUE ZN A 502
5AC5SOFTWAREGLU A:169 , HIS A:236 , LYS A:240BINDING SITE FOR RESIDUE ZN A 503
6AC6SOFTWAREHIS A:20 , GLU A:157 , HOH A:653 , HOH A:655BINDING SITE FOR RESIDUE ZN A 504
7AC7SOFTWAREGLU A:109 , ASP A:184 , GLU A:186 , HOH A:649BINDING SITE FOR RESIDUE ZN A 505
8AC8SOFTWAREHIS A:57 , PHE A:99 , LEU A:172 , TYR A:174 , PHE A:191 , LYS A:192 , GLY A:193 , ASP A:194 , SER A:195 , SER A:214 , TYR A:215 , GLY A:216 , ARG A:217 , ASN A:218 , ARG A:226 , HOH B:601 , HOH B:622BINDING SITE FOR CHAIN B OF ACETYL-ISOLEUCYL- GLUTAMYL-PROLYL-ASPARTYL-ALDEHYDE PEPTIDE
9AC9SOFTWAREGLU A:21 , ASN A:95 , ASN A:98 , SER A:100 , LYS A:111 , LYS A:148 , HIS A:173 , TYR A:174 , LYS A:243 , BMA A:307 , HOH A:637BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 301 TO 307

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:224 -Pro A:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_018371R55QGRAB_HUMANPolymorphism8192917AR48Q
2UniProtVAR_047409P94AGRAB_HUMANPolymorphism11539752AP88A
  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.GRAB_HUMAN21-245  1A:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.GRAB_HUMAN60-65  1A:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.GRAB_HUMAN197-208  1A:189-200

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002163411aENSE00001267008chr14:25103473-25103312162GRAB_HUMAN1-19190--
1.3bENST000002163413bENSE00000654543chr14:25102268-25102121148GRAB_HUMAN19-68501A:16-6148
1.5ENST000002163415ENSE00001762893chr14:25101665-25101530136GRAB_HUMAN68-113461A:61-107 (gaps)47
1.6bENST000002163416bENSE00000654540chr14:25101324-25101064261GRAB_HUMAN114-200871A:108-192 (gaps)89
1.7dENST000002163417dENSE00001929764chr14:25100420-25100161260GRAB_HUMAN201-247471A:193-244 (gaps)52

(-) 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 GRAB_HUMAN | P10144 from UniProtKB/Swiss-Prot  Length:247

    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      
          GRAB_HUMAN     21 IIGGHEAKPHSRPYMAYLMIWDQKSLKRCGGFLIRDDFVLTAAHCWGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKRTRAVQPLRLPSNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCESDLRHYYDSTIELCVGDPEIKKTSFKGDSGGPLVCNKVAQGIVSYGRNNGMPPRACTKVSSFVHWIKKTMKR  246
               SCOP domains d1iaua_ A: Granzyme B                                                                                                                                                                                                              SCOP domains
               CATH domains 1iauA01     1iauA02 A:28-120,A:233-244 Trypsin-like serine proteases                                      1iauA01 A:16-27,A:121-232 Trypsin-like serine proteases                                                     1iauA02      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee........eeeeeee....eeeeeeeeee..eeeehhhhh..eeeeee............eeeeeeeeee.............eeeee..........................eeeeee..............eeeeee..hhhhhhhhh........eeee................eeee..eeeeeeee........eeeee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------Q--------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 21-245                                                                                                                                                                                       - PROSITE (1)
                PROSITE (2) ---------------------------------------TRYPSI-----------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER -------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b  PDB: A:16-61 UniProt: 19-68          ---------------------------------------------Exon 1.6b  PDB: A:108-192 (gaps) UniProt: 114-200                                      Exon 1.7d  PDB: A:193-244 (gaps)               Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.5  PDB: A:61-107 (gaps) UniProt: 68-113------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                1iau A   16 IIGGHEAKPHSRPYMAYLMIWDQKSLKRCGGFLIRDDFVLTAAHCWGSSINVTLGAHNIKEQEPTQQFIPVKRPIPHPAYNPKNFSNDIMLLQLERKAKRTRAVQPLRLPSNKAQVKPGQTCSVAGWGQTAPLGKHSHTLQEVKMTVQEDRKCESDLRHYYDSTIELCVGDPEIKKTSFKGDSGGPLVCNKVAQGIVSYGRNNGMPPRACTKVSSFVHWIKKTMKR  244
                                    25        35 ||     43        53       |64        74        84        94       104       114       124       134       144 |  || 155       165       174      184A    |  192       202 ||    216    || 228       238      
                                               36A|                       61|                                                                               145A  ||                  172A        184A 188A              204|         221|                    
                                                36B                        63                                                                                   148|                                                      209          224                    
                                                                                                                                                                 151                                                                                          


Chain B from PDB  Type:PROTEIN  Length:5
                                      
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                1iau B  401 xIEPx  405
                            |   |
                          401-ACE
                              405-ASJ
   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
(-)
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 1IAU)

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GRAB_HUMAN | P10144)
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: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:0042267    natural killer cell mediated cytotoxicity    The directed killing of a target cell by a natural killer cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors.
    GO:1900740    positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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)

UniProtKB/Swiss-Prot
        GRAB_HUMAN | P10144: 1fq3

(-) Related Entries Specified in the PDB File

1fi8 RAT GRANZYME B WITH ECOTIN FRAGMENT
1fq3 HUMAN GRANZYME B (UNINHIBITED)