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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPERGILLOGLUTAMIC PEPTIDASE FROM ASPERGILLUS NIGER
 
Authors :  H. Sasaki, A. Nakagawa, S. Iwata, T. Muramatsu, M. Suganuma, Y. Sawano, K. Kubota, K. Takahashi
Date :  30 Nov 04  (Deposition) - 13 Dec 05  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aspergillopepsin Ii, Proctase A, Beta Sandwich Structure, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Sasaki, A. Nakagawa, T. Muramatsu, M. Suganuma, Y. Sawano, M. Kojima, K. Kubota, K. Takahashi, M. Tanokura
The Three-Dimensional Structure Of Aspergilloglutamic Peptidase From Aspergillus Niger
Proc. Jpn. Acad. , Ser. B V. 80 435 2004
PubMed: search

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:19 , ALA A:31 , TYR B:5 , TYR B:31 , GLU B:68BINDING SITE FOR RESIDUE SO4 B 201
2AC2SOFTWARESER A:4 , ASN A:6 , TRP A:7 , TYR B:48BINDING SITE FOR RESIDUE SO4 A 202
3AC3SOFTWAREGLU B:19 , ASP B:28 , CYS B:30 , SER B:37 , PRO B:46 , HOH B:206BINDING SITE FOR RESIDUE SO4 B 203
4AC4SOFTWAREASP B:28 , PHE B:112 , HOH B:281 , HOH B:282BINDING SITE FOR RESIDUE SO4 B 204
5AC5SOFTWARELYS B:64 , GLU B:80 , SER B:164 , GLY B:165 , HOH B:254BINDING SITE FOR RESIDUE SO4 B 205

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1B:6 -B:30
2B:18 -B:101

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y43)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y43)

(-) 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:32
 aligned with PRTA_ASPNG | P24665 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:32
                                    69        79        89  
           PRTA_ASPNG    60 EEYSSNWAGAVLIGDGYTKVTGEFTVPSVSAG  91
               SCOP domains d1y43.1 A:1-32,B:3-173           SCOP domains
               CATH domains -------------------------------- CATH domains
               Pfam domains -------------------------------- Pfam domains
         Sec.struct. author .eee..eeeeeee...eeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------- PROSITE
                 Transcript -------------------------------- Transcript
                 1y43 A   1 EEYSSNWAGAVLIGDGYTKVTGEFTVPSVSAG  32
                                    10        20        30  


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 d1y43.1 A:1-32,B:3-173 Aspergillopepsin II                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Peptidase_A4-1y43B01 B:3-173                                                                                                                                                Pfam domains (1)
           Pfam domains (2) Peptidase_A4-1y43B02 B:3-173                                                                                                                                                Pfam domains (2)
         Sec.struct. author .eeeeeeeeee........eeeeeeeeeee..eeeeeeeeeee....eee.........eeeeeeeeee..eeeeeeee....eeeeeee...........eeeeeee..ee..ee.ee....eeeeeeeeeee..eee.....eeeeeee..ee.eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1y43 B   3 EEYCASAWVGIDGDTCETAILQTGVDFCYEDGQTSYDAWYEWYPDYAYDFSDITISEGDSIKVTVEATSKSSGSATVENLTTGQSVTHTFSGNVEGDLCETNAEWIVEDFESGDSLVAFADFGSVTFTNAEATSGGSTVGPSDATVMDIEQDGSVLTETSVSGDSVTVTYV 173
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "CATH Domain" information available for 1Y43)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Peptidase_A4] (3)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  Cis Peptide Bonds
    Tyr B:45 - Pro B:46   [ RasMol ]  
 

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  1y43
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 Related Entries

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        PRTA_ASPNG | P24665: 3trs

(-) Related Entries Specified in the PDB File

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