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(-) Description

Title :  1.9 ANGSTROM CRYSTAL STRUCTURE OF A PLANT CYSTEINE PROTEASE ERVATAMIN C
 
Authors :  P. G. Thakurta, C. Chakrabarti, S. Biswas, J. K. Dattagupta
Date :  21 Feb 03  (Deposition) - 02 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Plant Cysteine Protease, Two Domain, Stable At Ph 2-12, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. G. Thakurta, S. Biswas, C. Chakrabarti, M. Sundd, M. V. Jagannadham J. K. Dattagupta
Structural Basis Of The Unusual Stability And Substrate Specificity Of Ervatamin C, A Plant Cysteine Protease From Ervatamia Coronaria
Biochemistry V. 43 1532 2004
PubMed-ID: 14769029  |  Reference-DOI: 10.1021/BI0357659

(-) Compounds

Molecule 1 - ERVATAMIN C
    Chains: A, B
    Organism Scientific: TABERNAEMONTANA DIVARICATA
    Organism Taxid: 52861

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1THJ2Ligand/IonTHIOSULFATE
2UNK2Mod. Amino Acid
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1THJ1Ligand/IonTHIOSULFATE
2UNK-1Mod. Amino Acid
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1THJ1Ligand/IonTHIOSULFATE
2UNK-1Mod. Amino Acid

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:23 , SER A:24 , CYS A:25 , HIS A:157 , HOH A:708BINDING SITE FOR RESIDUE THJ A 601
2AC2SOFTWAREGLY B:23 , SER B:24 , CYS B:25 , TRP B:26 , GLY B:66 , GLY B:158BINDING SITE FOR RESIDUE THJ B 601

(-) 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 1O0E)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.ERVC_TABDI19-30
 		  2A:19-30
B:19-30
2THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.ERVC_TABDI168-187
 		  2A:168-187
B:168-187
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.ERVC_TABDI19-30
 		  1A:19-30
-
2THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.ERVC_TABDI168-187
 		  1A:168-187
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.ERVC_TABDI19-30
 		  1-
B:19-30
2THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.ERVC_TABDI168-187
 		  1-
B:168-187

(-) Exons   (0, 0)

(no "Exon" information available for 1O0E)

(-) 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 ERVC_TABDI | P83654 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           ERVC_TABDI     1 LPEQIDWRKKGAVTPVKNQGSCGSCWAFSTVSTVESINQIRTGNLISLSEQELVDCDKKNHGCLGGAFVFAYQYIINNGGIDTQANYPYKAVQGPCQAASKVVSIDGYNGVPFCNEXALKQAVAVQPSTVAIDASSAQFQQYSSGIFSGPCGTKLNHGVTIVGYQANYWIVRNSWGRYWGEKGYIRMLRVGGCGLCGIARLPYYPTKA 208
               SCOP domains d1o0ea_ A: Ervatamin C                                                                                                                                                                                           SCOP domains
               CATH domains 1o0eA00 A:1-208 Cysteine proteinases                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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 ------------------THIOL_PROTEA-----------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTEASE_ASN  --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o0e A   1 LPEQIDWRKKGAVTPVKNQGSCGSCWAFSTVSTVESINQIRTGNLISLSEQELVDCDKKNHGCLGGAFVFAYQYIINNGGIDTQANYPYKAVQGPCQAASKVVSIDGYNGVPFCNExALKQAVAVQPSTVAIDASSAQFQQYSSGIFSGPCGTKLNHGVTIVGYQANYWIVRNSWGRYWGEKGYIRMLRVGGCGLCGIARLPYYPTKA 208
                                    10        20        30        40        50        60        70        80        90       100       110      |120       130       140       150       160       170       180       190       200        
                                                                                                                                              117-UNK                                                                                       


Chain B from PDB  Type:PROTEIN  Length:208
 aligned with ERVC_TABDI | P83654 from UniProtKB/Swiss-Prot  Length:208

    Alignment length:208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200        
           ERVC_TABDI     1 LPEQIDWRKKGAVTPVKNQGSCGSCWAFSTVSTVESINQIRTGNLISLSEQELVDCDKKNHGCLGGAFVFAYQYIINNGGIDTQANYPYKAVQGPCQAASKVVSIDGYNGVPFCNEXALKQAVAVQPSTVAIDASSAQFQQYSSGIFSGPCGTKLNHGVTIVGYQANYWIVRNSWGRYWGEKGYIRMLRVGGCGLCGIARLPYYPTKA 208
               SCOP domains d1o0eb_ B: Ervatamin C                                                                                                                                                                                           SCOP domains
               CATH domains 1o0eB00 B:1-208 Cysteine proteinases                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.hhhh............hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh...hhhhh.hhhhhhhhhhhhh...........................eeee....hhhhhhhhhhhh.eeeee...hhhhhh....ee.........eeeeeeeee..eeeee...........eeeee.....hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA-----------------------------------------------------------------------------------------------------------------------------------------THIOL_PROTEASE_ASN  --------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o0e B   1 LPEQIDWRKKGAVTPVKNQGSCGSCWAFSTVSTVESINQIRTGNLISLSEQELVDCDKKNHGCLGGAFVFAYQYIINNGGIDTQANYPYKAVQGPCQAASKVVSIDGYNGVPFCNExALKQAVAVQPSTVAIDASSAQFQQYSSGIFSGPCGTKLNHGVTIVGYQANYWIVRNSWGRYWGEKGYIRMLRVGGCGLCGIARLPYYPTKA 208
                                    10        20        30        40        50        60        70        80        90       100       110      |120       130       140       150       160       170       180       190       200        
                                                                                                                                              117-UNK
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1O0E)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ERVC_TABDI | P83654)
molecular function
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-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: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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1o0e
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        ERVC_TABDI | P83654: 2pns

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