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(-) Description

Title :  CRYSTAL STRUCTURE OF TRICHODERMA REESEI ASPARTIC PROTEINASE COMPLEXED WITH PEPSTATIN A
 
Authors :  A. S. Nascimento, S. Krauchenco, A. M. Golubev, A. Gustchina, A. Wlodaw I. Polikarpov
Date :  25 Sep 08  (Deposition) - 07 Oct 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trichoderma Reesei, Aspartic Proteinase, Aspartyl Protease, Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Nascimento, S. Krauchenco, A. M. Golubev, A. Gustchina, A. Wlodawer, I. Polikarpov
Statistical Coupling Analysis Of Aspartic Proteinases Based On Crystal Structures Of The Trichoderma Reesei Enzyme And Its Complex With Pepstatin A.
J. Mol. Biol. V. 382 763 2008
PubMed-ID: 18675276  |  Reference-DOI: 10.1016/J.JMB.2008.07.043

(-) Compounds

Molecule 1 - TRICHODERMA REESEI ASPARTIC PROTEASE
    Chains: A
    Fragment: UNP RESIDUES 79-407
    Organism Common: HYPOCREA JECORINA
    Organism Scientific: HYPOCREA JECORINA
    Organism Taxid: 51453
 
Molecule 2 - PEPSTATIN
    Chains: B
    Engineered: YES
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN STREPTOMYCES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1IVA1Mod. Amino AcidISOVALERIC ACID
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3STA2Mod. Amino AcidSTATINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:12 , ASP A:30 , ASP A:32 , GLY A:34 , SER A:35 , SER A:74 , TYR A:75 , GLY A:76 , ASP A:77 , SER A:79 , PHE A:189 , ASP A:215 , GLY A:217 , THR A:218 , THR A:219 , HOH A:515 , HOH A:761 , HOH A:896 , HOH B:937 , HOH B:939 , HOH B:940 , HOH B:942 , HOH B:943BINDING SITE FOR CHAIN B OF PEPSTATIN

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:250 -A:283

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Thr A:22 -Pro A:23
2Arg A:132 -Pro A:133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EMY)

(-) Exons   (0, 0)

(no "Exon" information available for 3EMY)

(-) 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:329
 aligned with Q2WBH2_HYPJE | Q2WBH2 from UniProtKB/TrEMBL  Length:407

    Alignment length:329
                                    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       398         
        Q2WBH2_HYPJE     79 QTGSAPNHPSDSADSEYITSVSIGTPAQVLPLDFDTGSSDLWVFSSETPKSSATGHAIYTPSKSSTSKKVSGASWSISYGDGSSSSGDVYTDKVTIGGFSVNTQGVESATRVSTEFVQDTVISGLVGLAFDSGNQVRPHPQKTWFSNAASSLAEPLFTADLRHGQNGSYNFGYIDTSVAKGPVAYTPVDNSQGFWEFTASGYSVGGGKLNRNSIDGIADTGTTLLLLDDNVVDAYYANVQSAQYDNQQEGVVFDCDEDLPSFSFGVGSSTITIPGDLLNLTPLEEGSSTCFGGLQSSSGIGINIFGDVALKAALVVFDLGNERLGWAQK  407
               SCOP domains d3emya_ A: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----3emyA01 A:2-170 Acid Proteases                                                                                                                                            3emyA02 A:171-326 Acid Proteases                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.......eeeeeee....eeeeeeee......ee.....hhhhhh.....hhhhh...eeeeeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeeeeeehhhhhhh....eeee..hhhhh........hhhhhhhh.....eeeee......eeeee...hhhhh....eeee........eeee..eee.........eeeee......eeehhhhhhhhhh.....eee....eeeee.......eeeee..eeeeehhhh.eeee......eeee.eee.......eehhhhhh.eeeeee....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3emy A   -2 xTGSAPNHPSDSADSEYITSVSIGTPAQVLPLDFDTGSSDLWVFSSETPKSSATGHAIYTPSKSSTSKKVSGASWSISYGDGSSSSGDVYTDKVTIGGFSVNTQGVESATRVSTEFVQDTVISGLVGLAFDSGNQVRPHPQKTWFSNAASSLAEPLFTADLRHGQNGSYNFGYIDTSVAKGPVAYTPVDNSQGFWEFTASGYSVGGGKLNRNSIDGIADTGTTLLLLDDNVVDAYYANVQSAQYDNQQEGVVFDCDEDLPSFSFGVGSSTITIPGDLLNLTPLEEGSSTCFGGLQSSSGIGINIFGDVALKAALVVFDLGNERLGWAQK  326
                            |        7        17        27        37        47        57      | 66        76    |   85        95       105       115       125      134A       144       154    || 166       176       185       195       204|  ||  216       226       236  |    245       255       265       275       283     ||297       307       317         
                            |                                                               63A               80A                                                   134A                      159|                   184A                203A |  ||                        238A                                         282A|    289|                                
                           -2-PCA                                                                                                                                                              162                                         204A  ||                                                                      282B     294                                
                                                                                                                                                                                                                                               207|                                                                                                                  
                                                                                                                                                                                                                                                211                                                                                                                  


Chain B 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
                3emy B  327 xVVxAx  332
                            |  | |
                          327-IVA|
                             330-STA
                               332-STA
   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 3EMY)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q2WBH2_HYPJE | Q2WBH2)
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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  3emy
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  Q2WBH2_HYPJE | Q2WBH2
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 Related Entries

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

UniProtKB/TrEMBL
        Q2WBH2_HYPJE | Q2WBH2: 3c9x

(-) Related Entries Specified in the PDB File

3c9x CRYSTAL STRUCTURE OF TRICHODERMA REESEI ASPARTIC PROTEINASE
3c9y CRYSTAL STRUCTURE OF TRICHODERMA REESEI ASPARTIC PROTEINASE COMPLEXED WITH PEPSTATIN A