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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF SUBTILISIN BPN' WITH CHYMOTRYPSIN INHIBITOR 2 M59R/E60S MUTANT
 
Authors :  E. S. Radisky, C. J. Lu, G. Kwan, D. E. Koshland Jr.
Date :  30 Nov 04  (Deposition) - 17 May 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Serine Protease; Inhibitor, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Radisky, C. J. Lu, G. Kwan, D. E. Koshland Jr.
Role Of The Intramolecular Hydrogen Bond Network In The Inhibitory Power Of Chymotrypsin Inhibitor 2
Biochemistry V. 44 6823 2005
PubMed-ID: 15865427  |  Reference-DOI: 10.1021/BI047301W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUBTILISIN BPN'
    Chains: E
    EC Number: 3.4.21.62
    Engineered: YES
    Expression System: BACILLUS SUBTILIS
    Expression System Plasmid: PSER25
    Expression System Strain: BG2036
    Expression System Taxid: 1423
    Expression System Vector Type: PLASMID
    Gene: APR
    Mutation: YES
    Organism Scientific: BACILLUS AMYLOLIQUEFACIENS
    Organism Taxid: 1390
    Synonym: SUBTILISIN NOVO
 
Molecule 2 - CHYMOTRYPSIN INHIBITOR 2
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCI2M59R-E60S
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HORDEUM VULGARE
    Organism Taxid: 4513

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric/Biological Unit (4, 5)
No.NameCountTypeFull Name
115P2Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2CA1Ligand/IonCALCIUM ION
3CIT1Ligand/IonCITRIC ACID
4NA1Ligand/IonSODIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN E:2 , ASP E:41 , LEU E:75 , ASN E:77 , ILE E:79 , VAL E:81BINDING SITE FOR RESIDUE CA E 1001
2AC2SOFTWARESER E:161 , 15P E:5001 , HOH E:5009BINDING SITE FOR RESIDUE NA E 1002
3AC3SOFTWARELEU E:209 , TYR E:214 , TYR E:217 , SER E:260 , HOH E:5075 , HOH E:5091 , HOH E:5140 , HOH E:5141 , HOH E:5183 , HOH E:5258 , HOH E:5286 , HOH E:5310BINDING SITE FOR RESIDUE CIT E 2001
4AC4SOFTWAREGLY E:160 , SER E:161 , PHE E:261 , TYR E:262 , NA E:1002BINDING SITE FOR RESIDUE 15P E 5001
5AC5SOFTWAREVAL E:143 , ALA E:144 , GLY E:146 , ASN E:243 , HOH E:5251BINDING SITE FOR RESIDUE 15P E 5002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y4A)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr E:167 -Pro E:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SUBT_BACAM_001 *Y128FSUBT_BACAM  ---  ---EY21F
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.SUBT_BACAM135-146  1E:28-39
2SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.SUBT_BACAM171-181  1E:64-74
3SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.SUBT_BACAM326-336  1E:219-229

(-) Exons   (0, 0)

(no "Exon" information available for 1Y4A)

(-) 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 E from PDB  Type:PROTEIN  Length:275
 aligned with SUBT_BACAM | P00782 from UniProtKB/Swiss-Prot  Length:382

    Alignment length:275
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377     
           SUBT_BACAM   108 AQSVPYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLKVAGGASMVPSETNPFQDNNSHGTHVAGTVAALNNSIGVLGVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGPSGSAALKAAVDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPSVIAVGAVDSSNQRASFSSVGPELDVMAPGVSIQSTLPGNKYGAYNGTSMASPHVAGAAALILSKHPNWTNTQVRSSLENTTTKLGDSFYYGKGLINVQAAAQ 382
               SCOP domains d1y4ae_ E: Subtilisin                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1y4aE00 E:1-275  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------Peptidase_S8-1y4aE01 E:27-275                                                                                                                                                                                                                             Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.......eeeeee...........eeeeee.............hhhhhhhhhhhh..............eeeeee......eehhhhhhhhhhhhhhh...eeee.ee....hhhhhhhhhhhhhh..eeeee......................eeeeee.................eeee...eeeee...eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.....hhhhhh....hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------F-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------SUBTILASE_AS------------------------SUBTILASE_H------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S---------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y4a E   1 AQSVPYGVSQIKAPALHSQGYTGSNVKVAVIDSGIDSSHPDLKVAGGASMVPSETNPFQDNNSHGTHVAGTVAALNNSIGVLGVAPSASLYAVKVLGADGSGQYSWIINGIEWAIANNMDVINMSLGGPSGSAALKAAVDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPSVIAVGAVDSSNQRASFSSVGPELDVMAPGVSIQSTLPGNKYGAYNGTSMASPHVAGAAALILSKHPNWTNTQVRSSLENTTTKLGDSFYYGKGLINVQAAAQ 275
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270     


Chain I from PDB  Type:PROTEIN  Length:63
 aligned with Q40059_HORVU | Q40059 from UniProtKB/TrEMBL  Length:84

    Alignment length:63
                                    31        41        51        61        71        81   
         Q40059_HORVU    22 KTEWPELVGKSVEEAKKVILQDKPAAQIIVLPVGTIVTMEYRIDRVRLFVDRLDNIAQVPRVG  84
               SCOP domains d1y4ai1 I:21-83 Chymotrypsin inhibitor CI-2                     SCOP domains
               CATH domains 1y4aI00 I:21-83 Trypsin Inhibitor V, subunit A                  CATH domains
               Pfam domains potato_inhibit-1y4aI01 I:21-83                                  Pfam domains
         Sec.struct. author ...hhhhh..hhhhhhhhhhhhh...eeeeee...eee...eeeeeeeee...........ee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 1y4a I  21 KTEWPELVGKSVEEAKKVILQDKPAAQIIVLPVGTIVTRSYRIDRVRLFVDRLDNIAQVPRVG  83
                                    30        40        50        60        70        80
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: CI-2 (32)
(-)
Clan: no clan defined [family: Peptidase_S8] (104)

(-) Gene Ontology  (14, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (SUBT_BACAM | P00782)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0042730    fibrinolysis    A process that solubilizes fibrin in the bloodstream of a multicellular organism, chiefly by the proteolytic action of plasmin.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    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.

Chain I   (Q40059_HORVU | Q40059)
molecular function
    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:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.

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  1y4a
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  SUBT_BACAM | P00782
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 Related Entries

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

UniProtKB/Swiss-Prot
        SUBT_BACAM | P00782: 1a2q 1ak9 1aqn 1au9 1dui 1gns 1gnv 1lw6 1s01 1s02 1sbh 1sbi 1sbn 1sbt 1sib 1spb 1st2 1sua 1sub 1suc 1sud 1sue 1sup 1tm1 1tm3 1tm4 1tm5 1tm7 1tmg 1to1 1to2 1ubn 1v5i 1y1k 1y33 1y34 1y3b 1y3c 1y3d 1y3f 1y48 1y4d 1yja 1yjb 1yjc 2sbt 2sic 2sni 2st1 3bgo 3cnq 3co0 3f49 3sic 5sic
UniProtKB/TrEMBL
        Q40059_HORVU | Q40059: 1tm1 1tm3 1tm4 1tm5 1tm7 1tmg 1to1 1to2 1y1k 1y33 1y34 1y3b 1y3c 1y3d 1y3f 1y48 1y4d

(-) Related Entries Specified in the PDB File

1y1k 1y33 1y34 1y3b 1y3c 1y3d 1y3f 1y48 1y4d