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(-) Description

Title :  THE STRUCTURE OF RAT MAST CELL PROTEASE II AT 1.9-ANGSTROMS RESOLUTION
 
Authors :  R. Reynolds, S. Remington, L. Weaver, R. Fischer, W. Anderson, H. Ammon, B. Matthews
Date :  10 Sep 84  (Deposition) - 29 Oct 84  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Serine Proteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Remington, R. G. Woodbury, R. A. Reynolds, B. W. Matthews, H. Neurath
The Structure Of Rat Mast Cell Protease Ii At 1. 9-A Resolution.
Biochemistry V. 27 8097 1988
PubMed-ID: 3233198  |  Reference-DOI: 10.1021/BI00421A019
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RAT MAST CELL PROTEASE II
    Chains: A, B
    Engineered: YES
    Organism Common: BLACK RAT
    Organism Scientific: RATTUS RATTUS
    Organism Taxid: 10117

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3RP2)

(-) Sites  (0, 0)

(no "Site" information available for 3RP2)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:42 -A:58
2A:136 -A:201
3A:168 -A:182
4B:42 -B:58
5B:136 -B:201
6B:168 -B:182

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:224A-Pro A:225
2Pro B:224A-Pro B:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RP2)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.MCPT2_RAT21-244
 		  2A:16-243
B:16-243
2TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.MCPT2_RAT61-66
 		  2A:53-58
B:53-58
3TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.MCPT2_RAT196-207
 		  2A:189-200
B:189-200

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000279881ENSRNOE00000299900chr15:34556079-3455613355MCPT2_RAT1-19190--
1.2ENSRNOT000000279882ENSRNOE00000302455chr15:34556641-34556791151MCPT2_RAT19-69512A:16-62 (gaps)
B:16-62 (gaps)		50
50
1.3ENSRNOT000000279883ENSRNOE00000326039chr15:34557309-34557444136MCPT2_RAT69-114462A:62-107
B:62-107		46
46
1.4ENSRNOT000000279884ENSRNOE00000201072chr15:34557648-34557902255MCPT2_RAT115-199852A:108-192 (gaps)
B:108-192 (gaps)		89
89
1.5ENSRNOT000000279885ENSRNOE00000201082chr15:34558267-34558413147MCPT2_RAT200-247482A:193-243 (gaps)
B:193-243 (gaps)		53
53

(-) 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:224
 aligned with MCPT2_RAT | P00770 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:224
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
           MCPT2_RAT     21 IIGGVESIPHSRPYMAHLDIVTEKGLRVICGGFLISRQFVLTAAHCKGREITVILGAHDVRKRESTQQKIKVEKQIIHESYNSVPNLHDIMLLKLEKKVELTPAVNVVPLPSPSDFIHPGAMCWAAGWGKTGVRDPTSYTLREVELRIMDEKACVDYRYYEYKFQVCVGSPTTLRAAFMGDSGGPLLCAGVAHGIVSYGHPDAKPPAIFTRVSTYVPWINAVIN  244
               SCOP domains d3rp2a_ A: Chymase II (mast cell proteinase II)                                                                                                                                                                                  SCOP domains
               CATH domains 3rp2A01     3rp2A02 A:28-120,A:233-241 Trypsin-like serine proteases                                       3rp2A01 A:16-27,A:121-232 Trypsin-like serine proteases                                                   3rp2A02  -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) ..............eeeeeee...eeeeeeeeeeee..eeeeee.....eeeeee...........eeeeee.................eeeeeee........................eeeeeee..............eeeeeeeehhhhh......hhhhh---...............eeeee..eeeeeeee........----hhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------eeee--------------------------------------eeeee------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: A:16-243 UniProt: 21-244                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: A:16-62 (gaps) UniProt: 19-69     ---------------------------------------------Exon 1.4  PDB: A:108-192 (gaps) UniProt: 115-199                                     Exon 1.5  PDB: A:193-243 (gaps)               Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.3  PDB: A:62-107 UniProt: 69-114       ---------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                3rp2 A   16 IIGGVESIPHSRPYMAHLDIVTEKGLRVICGGFLISRQFVLTAAHCKGREITVILGAHDVRKRESTQQKIKVEKQIIHESYNSVPNLHDIMLLKLEKKVELTPAVNVVPLPSPSDFIHPGAMCWAAGWGKTGVRDPTSYTLREVELRIMDEKACVDYRYYEYKFQVCVGSPTTLRAAFMGDSGGPLLCAGVAHGIVSYGHPDAKPPAIFTRVSTYVPWINAVIN  243
                                    25        35    ||| 42        52      ||63        73        83        93       103       113       123       133       143      |154       164      |172   || 184A    |  193       205||     221|   |  229       239    
                                                  39A||                  59|                                                                                      150|               170A|   176| 184A 188A          201| ||    216||   |                   
                                                   39B|                   61                                                                                       152                170B    180                     204 ||     221|   |                   
                                                    39C                                                                                                                                                                 206|     221A   |                   
                                                                                                                                                                                                                         209         224A                   


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with MCPT2_RAT | P00770 from UniProtKB/Swiss-Prot  Length:247

    Alignment length:224
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240    
           MCPT2_RAT     21 IIGGVESIPHSRPYMAHLDIVTEKGLRVICGGFLISRQFVLTAAHCKGREITVILGAHDVRKRESTQQKIKVEKQIIHESYNSVPNLHDIMLLKLEKKVELTPAVNVVPLPSPSDFIHPGAMCWAAGWGKTGVRDPTSYTLREVELRIMDEKACVDYRYYEYKFQVCVGSPTTLRAAFMGDSGGPLLCAGVAHGIVSYGHPDAKPPAIFTRVSTYVPWINAVIN  244
               SCOP domains d3rp2b_ B: Chymase II (mast cell proteinase II)                                                                                                                                                                                  SCOP domains
               CATH domains 3rp2B01     3rp2B02 B:28-120,B:233-241 Trypsin-like serine proteases                                       3rp2B01 B:16-27,B:121-232 Trypsin-like serine proteases                                                   3rp2B02  -- CATH domains
           Pfam domains (1) Trypsin-3rp2B01 B:16-238                                                                                                                                                                                                   ----- Pfam domains (1)
           Pfam domains (2) Trypsin-3rp2B02 B:16-238                                                                                                                                                                                                   ----- Pfam domains (2)
     Sec.struct. author (1) ..............eeeeeee...eeeeeeeeeeee..eeeeee.....eeeeee...........eeeeee.................eeeeeee........................eeeeeee..............eeeeeeeehhhhh......hhhhh---...............eeeee..eeeeeeee........----hhhhhhhhhhhhhh Sec.struct. author (1)
     Sec.struct. author (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------eeee--------------------------------------eeeee------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) TRYPSIN_DOM  PDB: B:16-243 UniProt: 21-244                                                                                                                                                                                       PROSITE (1)
                PROSITE (2) ----------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.2  PDB: B:16-62 (gaps) UniProt: 19-69     ---------------------------------------------Exon 1.4  PDB: B:108-192 (gaps) UniProt: 115-199                                     Exon 1.5  PDB: B:193-243 (gaps)               Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------Exon 1.3  PDB: B:62-107 UniProt: 69-114       ---------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                3rp2 B   16 IIGGVESIPHSRPYMAHLDIVTEKGLRVICGGFLISRQFVLTAAHCKGREITVILGAHDVRKRESTQQKIKVEKQIIHESYNSVPNLHDIMLLKLEKKVELTPAVNVVPLPSPSDFIHPGAMCWAAGWGKTGVRDPTSYTLREVELRIMDEKACVDYRYYEYKFQVCVGSPTTLRAAFMGDSGGPLLCAGVAHGIVSYGHPDAKPPAIFTRVSTYVPWINAVIN  243
                                    25        35    ||| 42        52      ||63        73        83        93       103       113       123       133       143      |154       164      |172   || 184A    |  193       205||     221|   |  229       239    
                                                  39A||                  59|                                                                                      150|               170A|   176| 184A 188A          201| ||    216||   |                   
                                                   39B|                   61                                                                                       152                170B    180                     204 ||     221|   |                   
                                                    39C                                                                                                                                                                 206|     221A   |                   
                                                                                                                                                                                                                         209         224A
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Beta Barrel (4804)
(-)
Topology: Thrombin, subunit H (1535)
(-)
Homologous Superfamily: Trypsin-like serine proteases (1488)
(-)
Black rat (Rattus rattus) (11)
1a3rp2A01A:16-27,A:121-232
1b3rp2B01B:16-27,B:121-232
1c3rp2A02A:28-120,A:233-241
1d3rp2B02B:28-120,B:233-241

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MCPT2_RAT | P00770)
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: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.

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    Pro A:224A - Pro A:225   [ RasMol ]  
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 Related Entries

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