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(-) Description

Title :  BINDING OF A REDUCED PEPTIDE INHIBITOR TO THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS. IMPLICATIONS FOR A MECHANISM OF ACTION
 
Authors :  K. Suguna, D. R. Davies
Date :  22 Jun 87  (Deposition) - 16 Jan 88  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Hydrolase, Aspartic Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Suguna, E. A. Padlan, C. W. Smith, W. D. Carlson, D. R. Davies
Binding Of A Reduced Peptide Inhibitor To The Aspartic Proteinase From Rhizopus Chinensis: Implications For A Mechanism Of Action.
Proc. Natl. Acad. Sci. Usa V. 84 7009 1987
PubMed-ID: 3313384  |  Reference-DOI: 10.1073/PNAS.84.20.7009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RHIZOPUSPEPSIN
    Chains: E
    EC Number: 3.4.23.6
    Engineered: YES
    Organism Scientific: RHIZOPUS MICROSPORUS VAR. CHINENSIS
    Organism Taxid: 4843
 
Molecule 2 - REDUCED PEPTIDE INHIBITOR
    Chains: I
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PUK1Mod. Amino AcidN-[(2S)-2-AMINO-3-PHENYLPROPYL]-L-PHENYLALANINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU E:16 , ASP E:33 , ASP E:35 , GLY E:37 , SER E:76 , TYR E:77 , GLY E:78 , ASP E:79 , SER E:81 , PHE E:114 , TRP E:194 , ASP E:218 , GLY E:220 , THR E:221 , THR E:222 , ILE E:225 , TRP E:294 , ILE E:298 , HOH I:578 , HOH I:874 , HOH I:876 , HOH I:877BINDING SITE FOR CHAIN I OF REDUCED PEPTIDE INHIBITOR
2CATAUTHORASP E:35 , ASP E:218CATALYTICALLY ACTIVE RESIDUES

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1E:48 -E:51
2E:252 -E:285

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr E:25 -Pro E:26
2Val E:315 -Pro E:316

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CARP_RHICH_001 *V83ICARP_RHICH  ---  ---EI15I
2UniProtVAR_CARP_RHICH_002 *K129NCARP_RHICH  ---  ---EN61N
3UniProtVAR_CARP_RHICH_003 *N184SCARP_RHICH  ---  ---ES116S
4UniProtVAR_CARP_RHICH_004 *S230KCARP_RHICH  ---  ---EK162K
5UniProtVAR_CARP_RHICH_005 *V298ICARP_RHICH  ---  ---EI230I
6UniProtVAR_CARP_RHICH_006 *S309YCARP_RHICH  ---  ---ES241Y
7UniProtVAR_CARP_RHICH_007 *N361DCARP_RHICH  ---  ---EN293D
8UniProtVAR_CARP_RHICH_008 *Q393ECARP_RHICH  ---  ---EE325E
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CARP_RHICH85-389  1E:17-321
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CARP_RHICH100-111
283-294		  2E:32-43
E:215-226

(-) Exons   (0, 0)

(no "Exon" information available for 3APR)

(-) 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:325
 aligned with CARP_RHICH | P06026 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:325
                                    78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388     
           CARP_RHICH    69 AGVGTVPMTDYGNDVEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCGSRQTKYDPKQSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAASFANGPNDGLLGLGFDTITTVRGVKTPMDNLISQGLISRPIFGVYLGKASNGGGGEYIFGGYDSTKFKGSLTTVPIDNSRGWWGITVDRATVGTSTVASSFDGILDTGTTLLILPNNVAASVARAYGASDNGDGTYTISCDTSRFKPLVFSINGASFQVSPDSLVFEEYQGQCIAGFGYGNFDFAIIGDTFLKNNYVVFNQGVPEVQIAPVAQ 393
               SCOP domains d3apre_ E: Acid protease                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains -----3aprE01 E:6-174 Acid Proteases                                                                                                                                           3aprE02 E:175-323 Acid Proteases                                                                                                                     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee....eeeeeeeee...eeeeeeee....eeeee...............hhh....ee..eeeeee.....eeeeeeeeeeeee..eeee.eeeeeeeeeehhhh.....eeee...hhh........hhhhhhh.......eeeeee..hhh...eeeee....hhh.....eeee........eeee.eeee..eeee..eeeee......eeee.hhhhhhhhh...eee...eeee.........eeeee..eeeee.hhhh..eee..eeee.eeee..eeeeeehhhh..eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------I---------------------------------------------N------------------------------------------------------S---------------------------------------------K-------------------------------------------------------------------I----------Y---------------------------------------------------D-------------------------------E SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: E:17-321 UniProt: 85-389                                                                                                                                                                                                                                                                      ---- PROSITE (1)
                PROSITE (2) -------------------------------ASP_PROTEASE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE--------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3apr E   1 AGVGTVPMTDYGNDIEYYGQVTIGTPGKKFNLDFDTGSSDLWIASTLCTNCGSGQTKYDPNQSSTYQADGRTWSISYGDGSSASGILAKDNVNLGGLLIKGQTIELAKREAASFASGPNDGLLGLGFDTITTVRGVKTPMDNLISQGLISRPIFGVYLGKAKNGGGGEYIFGGYDSTKFKGSLTTVPIDNSRGWWGITVDRATVGTSTVASSFDGILDTGTTLLILPNNIAASVARAYGASDNGDGTYTISCDTSAFKPLVFSINGASFQVSPDSLVFEEFQGQCIAGFGYGNWGFAIIGDTFLKNNYVVFNQGVPEVQIAPVAE 325
                                    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       280       290       300       310       320     


Chain I from PDB  Type:PROTEIN  Length:6
                                      
               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
                 3apr I   2 PFHxVY   7
                               |  
                               5-PUK
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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
(-)
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 3APR)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (CARP_RHICH | P06026)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    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.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CARP_RHICH | P06026: 1uh7 1uh8 1uh9 2apr 4apr 5apr 6apr

(-) Related Entries Specified in the PDB File

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