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(-) Description

Title :  GLYCYL ENDOPEPTIDASE-COMPLEX WITH BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE COVALENTLY BOUND TO CYSTEINE 25
 
Authors :  B. P. Ohara, A. M. Hemmings, D. J. Buttle, L. H. Pearl
Date :  25 May 95  (Deposition) - 07 Dec 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. P. O'Hara, A. M. Hemmings, D. J. Buttle, L. H. Pearl
Crystal Structure Of Glycyl Endopeptidase From Carica Papaya: A Cysteine Endopeptidase Of Unusual Substrate Specificity.
Biochemistry V. 34 13190 1995
PubMed-ID: 7548082  |  Reference-DOI: 10.1021/BI00040A034

(-) Compounds

Molecule 1 - GLYCYL ENDOPEPTIDASE
    Chains: E
    EC Number: 3.4.22.25
    Organism Common: PAPAYA
    Organism Scientific: CARICA PAPAYA
    Organism Taxid: 3649
 
Molecule 2 - BENZYLOXYCARBONYL-LEUCINE-VALINE-GLYCINE-METHYLENE 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  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
10HQ1Mod. Amino AcidDIAZOMETHANE
2PHQ1Mod. Amino AcidBENZYL CHLOROCARBONATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS E:18 , GLY E:20 , GLU E:23 , CYS E:25 , TRP E:26 , ARG E:65 , GLY E:66 , TYR E:67 , VAL E:157 , ASP E:158 , HOH E:229 , HOH E:257 , HOH I:30BINDING SITE FOR CHAIN I OF BENZYLOXYCARBONYL- LEUCINE-VALINE-GLYCINE-METHYLENE

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1E:22 -E:63
2E:56 -E:95
3E:153 -E:204

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1GEC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.PAPA4_CARPA151-162  1E:19-30
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.PAPA4_CARPA289-299  1E:157-167
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.PAPA4_CARPA306-325  1E:174-193

(-) Exons   (0, 0)

(no "Exon" information available for 1GEC)

(-) 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:216
 aligned with PAPA4_CARPA | P05994 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:216
                                   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342      
          PAPA4_CARPA   133 LPESVDWRAKGAVTPVKHQGYCESCWAFSTVATVEGINKIKTGNLVELSEQELVDCDKQSYGCNRGYQSTSLQYVAQNGIHLRAKYPYIAKQQTCRANQVGGPKVKTNGVGRVQSNNEGSLLNAIAHQPVSVVVESAGRDFQNYKGGIFEGSCGTKVDHAVTAVGYGKSGGKGYILIKNSWGPGWGENGYIRIRRASGNSPGVCGVYRSSYYPIKN 348
               SCOP domains d1gece_ E: Glycyl endopeptidase                                                                                                                                                                                          SCOP domains
               CATH domains 1gecE00 E:1-216 Cysteine proteinases                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........................hhhhhhhhhhhhhhhhhh.......hhhhhhh...........hhhhhhhhhhh..................hhhh........eeee.....hhhhhhhhhh..eeeee....hhhh................eeeeeeeeeee..eeeeeee...........eeeee........hhh.....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE------THIOL_PROTEASE_ASN  ----------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1gec E   1 LPESVDWRAKGAVTPVKHQGYCESCWAFSTVATVEGINKIKTGNLVELSEQELVDCDLQSYGCNRGYQSTSLQYVAQNGIHLRAKYPYIAKQQTCRANQVGGPKVKTNGVGRVQSNNEGSLLNAIAHQPVSVVVESAGRDFQNYKGGIFEGSCGTKVDHAVTAVGYGKSGGKGYILIKNSWGPGWGENGYIRIRRASGNSPGVCGVYRSSYYPIKN 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain I from PDB  Type:PROTEIN  Length:5
                                     
               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
                 1gec I   1 xLVGx   5
                            |   |
                            1-PHQ
                                5-0HQ
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GEC)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (PAPA4_CARPA | P05994)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue 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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