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(-) Description

Title :  CRYSTAL STRUCTURE OF PLANT CYSTEINE PROTEASE ERVATAMIN-C COMPLEXED WITH IRREVERSIBLE INHIBITOR E-64 AT 2.7 A RESOLUTION
 
Authors :  R. Ghosh, C. Chakrabarti, J. K. Dattagupta, S. Biswas
Date :  04 May 07  (Deposition) - 22 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protease-Inhibitor Complex, Papain-Like Fold, Plant Cysteine Protease, Ervatamin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ghosh, S. Chakraborty, C. Chakrabarti, J. K. Dattagupta, S. Biswas
Structural Insights Into The Substrate Specificity And Activity Of Ervatamins, The Papain-Like Cysteine Proteases From A Tropical Plant, Ervatamia Coronaria.
Febs J. V. 275 421 2008
PubMed-ID: 18167146  |  Reference-DOI: 10.1111/J.1742-4658.2007.06211.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ERVATAMIN-C
    Chains: A, B
    EC Number: 3.4.22.-
    Organism Scientific: TABERNAEMONTANA DIVARICATA
    Organism Taxid: 52861
    Other Details: TROPICAL FLOWERING PLANT

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1E642Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1E641Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1E641Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
2SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:192 , HOH A:375 , LYS B:154BINDING SITE FOR RESIDUE SO4 A 305
2AC2SOFTWARECYS A:63 , VAL A:92 , GLN A:93 , HOH A:370BINDING SITE FOR RESIDUE SO4 A 307
3AC3SOFTWARECYS A:56 , ASN A:57 , LYS A:58 , LYS A:59 , TYR A:74BINDING SITE FOR RESIDUE SO4 A 308
4AC4SOFTWAREGLN A:19 , GLY A:23 , SER A:24 , CYS A:25 , TRP A:26 , HIS A:61 , LYS A:64 , GLY A:65 , GLY A:66 , ASN A:156 , HIS A:157 , HOH A:356 , HOH A:357 , HOH A:367BINDING SITE FOR RESIDUE E64 A 302
5AC5SOFTWARELYS A:154 , GLY B:191 , GLY B:192 , HOH B:357BINDING SITE FOR RESIDUE SO4 B 303
6AC6SOFTWARECYS B:56 , ASN B:57 , LYS B:58 , LYS B:59 , TYR B:74BINDING SITE FOR RESIDUE SO4 B 304
7AC7SOFTWAREASN A:44 , LYS B:101 , GLN B:182 , HOH B:356BINDING SITE FOR RESIDUE SO4 B 306
8AC8SOFTWAREGLN B:19 , GLY B:23 , SER B:24 , CYS B:25 , TRP B:26 , HIS B:61 , LYS B:64 , GLY B:65 , GLY B:66 , ASN B:156 , HIS B:157 , GLY B:158BINDING SITE FOR RESIDUE E64 B 301

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:63
2A:56 -A:96
3A:114 -A:193
4A:151 -A:196
5B:22 -B:63
6B:56 -B:96
7B:114 -B:193
8B:151 -B:196

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:149 -Pro A:150
2Gly B:149 -Pro B:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PRE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PRE)

(-) Exons   (0, 0)

(no "Exon" information available for 2PRE)

(-) 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:208
 aligned with A8DS38_TABDI | A8DS38 from UniProtKB/TrEMBL  Length:365

    Alignment length:208
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333        
         A8DS38_TABDI   134 LPEQIDWRKKGAVTPVKNQGKCGSCWAFSTVSTVESINQIRTGNLISLSEQQLVDCNKKNHGCKGGAFVYAYQYIIDNGGIDTEANYPYKAVQGPCRAAKKVVRIDGYKGVPHCNENALKKAVASQPSVVAIDASSKQFQHYKSGIFSGPCGTKLNHGVVIVGYWKDYWIVRNSWGRYWGEQGYIRMKRVGGCGLCGIARLPYYPTKA 341
               SCOP domains d2prea_ A: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2preA00 A:1-208 Cysteine proteinases                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.................hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhh............................eeee....hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeeee..eeeee...........eeeee.....hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pre A   1 LPEQIDWRKKGAVTPVKNQGKCGSCWAFSTVSTVESINQIRTGNLISLSEQQLVDCNKKNHGCKGGAFVYAYQYIIDNGGIDTEANYPYKAVQGPCRAAKKVVRIDGYKGVPHCNENALKKAVASQPSVVAIDASSKQFQHYKSGIFSGPCGTKLNHGVVIVGYWKDYWIVRNSWGRYWGEQGYIRMKRVGGCGLCGIARLPYYPTKA 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with A8DS38_TABDI | A8DS38 from UniProtKB/TrEMBL  Length:365

    Alignment length:208
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333        
         A8DS38_TABDI   134 LPEQIDWRKKGAVTPVKNQGKCGSCWAFSTVSTVESINQIRTGNLISLSEQQLVDCNKKNHGCKGGAFVYAYQYIIDNGGIDTEANYPYKAVQGPCRAAKKVVRIDGYKGVPHCNENALKKAVASQPSVVAIDASSKQFQHYKSGIFSGPCGTKLNHGVVIVGYWKDYWIVRNSWGRYWGEQGYIRMKRVGGCGLCGIARLPYYPTKA 341
               SCOP domains d2preb_ B: automated matches                                                                                                                                                                                     SCOP domains
               CATH domains 2preB00 B:1-208 Cysteine proteinases                                                                                                                                                                             CATH domains
           Pfam domains (1) Peptidase_C1-2preB01 B:1-206                                                                                                                                                                                  -- Pfam domains (1)
           Pfam domains (2) Peptidase_C1-2preB02 B:1-206                                                                                                                                                                                  -- Pfam domains (2)
         Sec.struct. author ....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh...........................eeee....hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeee...eeeee...........eeeee.....hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pre B   1 LPEQIDWRKKGAVTPVKNQGKCGSCWAFSTVSTVESINQIRTGNLISLSEQQLVDCNKKNHGCKGGAFVYAYQYIIDNGGIDTEANYPYKAVQGPCRAAKKVVRIDGYKGVPHCNENALKKAVASQPSVVAIDASSKQFQHYKSGIFSGPCGTKLNHGVVIVGYWKDYWIVRNSWGRYWGEQGYIRMKRVGGCGLCGIARLPYYPTKA 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Peptidase_CA (169)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (A8DS38_TABDI | A8DS38)
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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(-) Related Entries Specified in the PDB File

1o0e CRYSTAL STRUCTURE OF THIOSULFATE INACTIVED ERVATAMIN-C
2pns CRYSTAL STRUCTURE OF THIOSULFATE INACTIVATED ERVATAMIN-C, REFINED WITH CDNA-DERIVED AMINO ACID SEQUENCE