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(-) Description

Title :  CRYSTAL STRUCTURE OF ASPARTIC PROTEINASE FROM IRPEX LACTEUS
 
Authors :  Z. Fujimoto, Y. Fujii, S. Kaneko, H. Kobayashi, H. Mizuno
Date :  02 Jun 04  (Deposition) - 07 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,I
Keywords :  Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Fujimoto, Y. Fujii, S. Kaneko, H. Kobayashi, H. Mizuno
Crystal Structure Of Aspartic Proteinase From Irpex Lacteus In Complex With Inhibitor Pepstatin
J. Mol. Biol. V. 341 1227 2004
PubMed-ID: 15321718  |  Reference-DOI: 10.1016/J.JMB.2004.06.049

(-) Compounds

Molecule 1 - POLYPOROPEPSIN
    Chains: A
    EC Number: 3.4.23.29
    Organism Scientific: IRPEX LACTEUS
    Organism Taxid: 5319
    Synonym: ASPARTIC PROTEINASE
 
Molecule 2 - PEPSTATIN
    Chains: I
    Engineered: YES
    Other Details: CHEMICALLY SYNTHESIZED
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1IVA1Mod. Amino AcidISOVALERIC ACID
2SO47Ligand/IonSULFATE ION
3STA2Mod. Amino AcidSTATINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:177 , PRO A:178 , GLY A:261 , GLY A:262 , HOH A:978 , HOH A:1278 , HOH A:1355 , HOH A:1364 , HOH A:1385 , HOH A:1419 , HOH A:1453BINDING SITE FOR RESIDUE SO4 A 901
2AC2SOFTWARELYS A:58 , GLY A:70 , THR A:71 , SER A:93 , HOH A:1275 , HOH A:1482BINDING SITE FOR RESIDUE SO4 A 902
3AC3SOFTWARELYS A:48 , SER A:194 , SER A:205 , SER A:206 , HOH A:959 , HOH A:1022 , HOH A:1036 , HOH A:1085 , HOH A:1392 , HOH A:1550BINDING SITE FOR RESIDUE SO4 A 903
4AC4SOFTWARESER A:81 , ARG A:94 , ASP A:95 , HOH A:1015 , HOH A:1363 , HOH A:1454 , HOH A:1480BINDING SITE FOR RESIDUE SO4 A 904
5AC5SOFTWAREGLY A:97 , HOH A:1203 , HOH A:1316 , HOH A:1480 , HOH A:1488BINDING SITE FOR RESIDUE SO4 A 905
6AC6SOFTWAREHIS A:120 , THR A:121 , SER A:122 , THR A:123 , HOH A:1009BINDING SITE FOR RESIDUE SO4 A 906
7AC7SOFTWARETHR A:336 , HOH A:956 , HOH A:1331 , HOH A:1342 , HOH A:1411BINDING SITE FOR RESIDUE SO4 A 907
8AC8SOFTWAREVAL A:12 , LEU A:30 , ASP A:32 , GLY A:34 , THR A:62 , TYR A:63 , GLY A:64 , SER A:65 , TYR A:188 , ASP A:212 , GLY A:214 , THR A:215 , THR A:216 , LEU A:304 , ILE A:307 , HOH A:1045 , HOH I:30 , HOH I:221 , HOH I:290 , HOH I:417 , HOH I:424 , HOH I:530BINDING SITE FOR CHAIN I OF PEPSTATIN

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:22 -Pro A:23
2Ser A:118 -Pro A:119
3Ser A:183 -Pro A:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.CARP_IRPLA14-330  1A:14-330
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.CARP_IRPLA29-40
209-220		  2A:29-40
A:209-220

(-) Exons   (0, 0)

(no "Exon" information available for 1WKR)

(-) 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:340
 aligned with CARP_IRPLA | P17576 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:340
                                    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       330       340
           CARP_IRPLA     1 AAGSVPATNQLVDYVVNVGVGSPATTYSLLVDTGSSNTWLGADKSYVKTSTSSATSDKVSVTYGSGSFSGTEYTDTVTLGSLTIPKQSIGVASRDSGFDGVDGILGVGPVDLTVGTLSPHTSTSIPTVTDNLFSQGTIPTNLLAVSFEPTTSESSTNGELTFGATDSSKYTGSITYTPITSTSPASAYWGINQTIRYGSSTSILSSTAGIVDTGTTLTLIASDAFAKYKKATGAVADNNTGLLRLTTAQYANLQSLFFTIGGQTFELTANAQIWPRNLNTAIGGSASSVYLIVGDLGSDSGEGLDFINGLTFLERFYSVYDTTNKRLGLATTSFTTATSN 340
               SCOP domains d1wkra_ A: Acid protease                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1wkrA01 A:1-170 Acid Proteases                                                                                                                                            1wkrA02 A:171-340 Acid Proteases                                                                                                                                           CATH domains
               Pfam domains ------------Asp-1wkrA01 A:13-332                                                                                                                                                                                                                                                                                                            -------- Pfam domains
         Sec.struct. author ..eeeeeee....eeeeeee....eeeeeeee......ee............eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeeeeee......eeee..hhhhhh..ee........hhhhhhhhh......eeeee........eeeeeeee...hhhhh....eeee.....hhhhh.eeeeeeee...eeeeeeeeeee......eeehhhhhhhhhhhhh.ee......eeehhhhhhh...eeeee..eeeee.hhhhh.hhhhhhhhh.....ee..eee..........eeehhhhhh.eeeeee....eeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------PEPTIDASE_A1  PDB: A:14-330 UniProt: 14-330                                                                                                                                                                                                                                                                                  ---------- PROSITE (1)
                PROSITE (2) ----------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wkr A   1 AAGSVPATNQLVDYVVNVGVGSPATTYSLLVDTGSSNTWLGADKSYVKTSTSSATSDKVSVTYGSGSFSGTEYTDTVTLGSLTIPKQSIGVASRDSGFDGVDGILGVGPVDLTVGTLSPHTSTSIPTVTDNLFSQGTIPTNLLAVSFEPTTSESSTNGELTFGATDSSKYTGSITYTPITSTSPASAYWGINQSIRYGSSTSILSSTAGIVDTGTTLTLIASDAFAKYKKATGAVADNNTGLLRLTTAQYANLQSLFFTIGGQTFELTANAQIWPRNLNTAIGGSASSVYLIVGDLGSDSGEGLDFINGLTFLERFYSVYDTTNKRLGLATTSFTTATSN 340
                                    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       330       340


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
                 1wkr I 801 xVVxAx 806
                            |  | |
                          801-IVA|
                             804-STA
                               806-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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_AA (368)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CARP_IRPLA | P17576)
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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