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(-) Description

Title :  THE CRYSTAL STRUCTURE OF ASPERGILLOGLUTAMIC PEPTIDASE FROM ASPERGILLUS NIGER
 
Authors :  H. Sasaki, K. Kubota, W. C. Lee, J. Ohtsuka, M. Kojima, K. Takahashi, M. T
Date :  10 Sep 11  (Deposition) - 22 Aug 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Aspergilloglutamic Peptidase, Glutamic Peptidase, Beta Sandwich Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sasaki, K. Kubota, W. C. Lee, J. Ohtsuka, M. Kojima, S. Iwata, A. Nakagawa, K. Takahashi, M. Tanokura
The Crystal Structure Of An Intermediate Dimer Of Aspergilloglutamic Peptidase That Mimics The Enzyme-Activation Product Complex Produced Upon Autoproteolysis.
J. Biochem. V. 152 45 2012
PubMed-ID: 22569035  |  Reference-DOI: 10.1093/JB/MVS050

(-) Compounds

Molecule 1 - ASPERGILLOPEPSIN-2 LIGHT CHAIN
    Chains: A, C
    EC Number: 3.4.23.19
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 29838
    Strain: VAR. MACROSPORUS
    Synonym: ASPERGILLOPEPSIN II LIGHT CHAIN
 
Molecule 2 - ASPERGILLOPEPSIN-2 HEAVY CHAIN
    Chains: B, D
    EC Number: 3.4.23.19
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 29838
    Strain: VAR. MACROSPORUS
    Synonym: ASPERGILLOPEPSIN II HEAVY CHAIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1DMS2Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1DMS1Ligand/IonDIMETHYL SULFOXIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:7 , GLY B:15 , ASP B:16 , MET B:149BINDING SITE FOR RESIDUE DMS A 201
2AC2SOFTWARETYR D:50 , HIS D:90 , PHE D:92 , SER D:156 , HOH D:184 , HOH D:221 , HOH D:224 , HOH D:233BINDING SITE FOR RESIDUE DMS D 200

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1B:6 -B:30
2B:18 -B:101
3D:6 -D:30
4D:18 -D:101

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr B:45 -Pro B:46
2Tyr D:45 -Pro D:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TRS)

(-) Sequences/Alignments

Asymmetric 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:37
 aligned with PRTA_ASPNG | P24665 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:37
                                    70        80        90       
           PRTA_ASPNG    61 EYSSNWAGAVLIGDGYTKVTGEFTVPSVSAGSSGSSG  97
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author .ee..eeeeeee...eeeeeeeee..........ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 3trs A   2 EYSSNWAGAVLIGDGYTKVTGEFTVPSVSAGSSGSSG  38
                                    11        21        31       


Chain B from PDB  Type:PROTEIN  Length:171
 aligned with PRTA_ASPNG | P24665 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:171
                                   121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281 
           PRTA_ASPNG   112 EEYCASAWVGIDGDTCETAILQTGVDFCYEDGQTSYDAWYEWYPDYAYDFSDITISEGDSIKVTVEATSKSSGSATVENLTTGQSVTHTFSGNVEGDLCETNAEWIVEDFESGDSLVAFADFGSVTFTNAEATSGGSTVGPSDATVMDIEQDGSVLTETSVSGDSVTVTYV 282
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee........eeeeeeeeeee..eeeeeeeeeee...eeee.........eeeeeeeeee..eeeeeeee....eeeeeee...........eeeeeee..ee..ee.ee....eeeeeeeeeee..eeehhhhheeeeeee..ee.eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3trs B   3 EEYCASAWVGIDGDTCETAILQTGVDFCYEDGQTSYDAWYEWYPDYAYDFSDITISEGDSIKVTVEATSKSSGSATVENLTTGQSVTHTFSGNVEGDLCETNAEWIVEDFESGDSLVAFADFGSVTFTNAEATSGGSTVGPSDATVMDIEQDGSVLTETSVSGDSVTVTYV 173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 


Chain C from PDB  Type:PROTEIN  Length:30
 aligned with PRTA_ASPNG | P24665 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:30
                                    70        80        90
           PRTA_ASPNG    61 EYSSNWAGAVLIGDGYTKVTGEFTVPSVSA  90
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author .ee..eeeeeee...eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 3trs C   2 EYSSNWAGAVLIGDGYTKVTGEFTVPSVSA  31
                                    11        21        31


Chain D from PDB  Type:PROTEIN  Length:170
 aligned with PRTA_ASPNG | P24665 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:170
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282
           PRTA_ASPNG   113 EYCASAWVGIDGDTCETAILQTGVDFCYEDGQTSYDAWYEWYPDYAYDFSDITISEGDSIKVTVEATSKSSGSATVENLTTGQSVTHTFSGNVEGDLCETNAEWIVEDFESGDSLVAFADFGSVTFTNAEATSGGSTVGPSDATVMDIEQDGSVLTETSVSGDSVTVTYV 282
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee........eeeeeeeeeee..eeeeeeeeeee....ee..........eeeeeeeeee..eeeeeeee....eeeeeee...........eeeeeee..ee..ee.ee....eeeeeeeeeee..eee.....eeeeeee..ee.eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3trs D   4 EYCASAWVGIDGDTCETAILQTGVDFCYEDGQTSYDAWYEWYPDYAYDFSDITISEGDSIKVTVEATSKSSGSATVENLTTGQSVTHTFSGNVEGDLCETNAEWIVEDFESGDSLVAFADFGSVTFTNAEATSGGSTVGPSDATVMDIEQDGSVLTETSVSGDSVTVTYV 173
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173
   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  (0, 0)

(no "SCOP Domain" information available for 3TRS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TRS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TRS)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PRTA_ASPNG | P24665)
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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        PRTA_ASPNG | P24665: 1y43

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