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(-) Description

Title :  THE HIGH RESOLUTION X-RAY STRUCTURE OF PAPAIN COMPLEXED WITH FRAGMENTS OF THE TRYPANOSOMA BRUCEI CYSTEINE PROTEASE INHIBITOR ICP.
 
Authors :  M. S. Alphey, W. N. Hunter
Date :  24 Mar 06  (Deposition) - 18 May 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase/Inhibitor, Complex Hydrolase/Inhibitor, Icp, Cysteine Protease, Inhibitor, Trypanosoma Brucei, Allergen, Protease, Thiol Protease, Zymogen, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Alphey, W. N. Hunter
High-Resolution Complex Of Papain With Remnants Of A Cysteine Protease Inhibitor Derived From Trypanosoma Brucei
Acta Crystallogr. , Sect. F V. 62 504 2006
PubMed-ID: 16754967  |  Reference-DOI: 10.1107/S1744309106014849

(-) Compounds

Molecule 1 - PAPAIN
    Chains: A
    EC Number: 3.4.22.2
    Organism Scientific: CARICA PAPAYA
    Organism Taxid: 3649
    Other Details: PURCHASED FROM SIGMA
    Synonym: PAPAYA PROTEINASE I, PPI, ALLERGEN, CARP1PAPAIN
 
Molecule 2 - INHIBITOR OF CYSTEINE PEPTIDASE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBP117
    Expression System Strain: C43
    Expression System Taxid: 562
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Other Details: TWO PEPTIDE FRAGMENTS FROM DIGESTION OF ICP
    Synonym: CYSTEINE PROTEASE INHIBITOR, ICP

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3OCS1Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:17 , ASN A:18 , ARG A:83 , ARG A:93 , TYR A:94 , HOH A:2014BINDING SITE FOR RESIDUE ACT A1218
2AC2SOFTWAREGLU A:3 , ARG A:59 , GLY A:138 , LYS A:139 , ASP A:140 , HOH A:2121BINDING SITE FOR RESIDUE ACT A1219
3AC3SOFTWARECYS A:56 , TYR A:78 , CYS A:95 , ARG A:98 , GOL A:1217 , HOH A:2158BINDING SITE FOR RESIDUE ACT A1220
4AC4SOFTWAREVAL A:13 , THR A:14 , PRO A:15 , VAL A:16 , TYR A:186BINDING SITE FOR RESIDUE GOL A1216
5AC5SOFTWAREGLU A:3 , TYR A:4 , ARG A:59 , GLN A:73 , LEU A:74 , GLN A:77 , TYR A:78 , ACT A:1220 , HOH A:2004 , HOH A:2047 , HOH A:2050 , HOH A:2064BINDING SITE FOR RESIDUE GOL A1217

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:22 -A:63
2A:56 -A:95
3A:153 -A:200

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:151 -Pro A:152
2Lys A:211 -Asn A:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.PAPA1_CARPA152-163  1A:19-30
2THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.PAPA1_CARPA290-300  1A:157-167
3THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.PAPA1_CARPA303-322  1A:170-189

(-) Exons   (0, 0)

(no "Exon" information available for 2CIO)

(-) 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:212
 aligned with PAPA1_CARPA | P00784 from UniProtKB/Swiss-Prot  Length:345

    Alignment length:212
                                   143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343  
          PAPA1_CARPA   134 IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 345
               SCOP domains d2cioa_ A: Papain                                                                                                                                                                                                    SCOP domains
               CATH domains 2cioA00 A:1-212 Cysteine proteinases                                                                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee...................hhhhhhhhhhhhhhhhhh.....hhhhhhhhh.........hhhhhhhhhhhh..............................eeee....hhhhhhhhhhhh.eeeee...hhhhhh...............eeeeeeeee..eeeee...........eeeee.......hhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--THIOL_PROTEASE_ASN  ----------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cio A   1 IPEYVDWRQKGAVTPVKNQGSCGScWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN 212
                                    10        20    |   30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
                                                   25-OCS                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:7
 aligned with Q868H0_9TRYP | Q868H0 from UniProtKB/TrEMBL  Length:121

    Alignment length:21
                                    87        97 
         Q868H0_9TRYP    78 GGTMVLEVKALKAGKHTLSLA  98
               SCOP domains d2c              iob_ SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ...--------------.... Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 2cio B  78 GGT--------------LSLA  98
                              |      -       |97 
                             80             95
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
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 2CIO)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAPA1_CARPA | P00784)
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.
    GO:0097655    serpin family protein binding    Interacting selectively and non-covalently with any member of the serpin protein family (serine protease inhibitors or classified inhibitor family I4). Serpins are a broadly distributed family of protease inhibitors that use a conformational change to inhibit target enzymes. They are central in controlling many important proteolytic cascades. The majority of serpins inhibit serine proteases, but serpins that inhibit caspases and papain-like cysteine proteases have also been identified. Rarely, serpins perform a non-inhibitory function; for example, several human serpins function as hormone transporters and certain serpins function as molecular chaperones or tumor suppressors.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Chain B   (Q868H0_9TRYP | Q868H0)

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  Q868H0_9TRYP | Q868H0
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PAPA1_CARPA | P00784: 1bp4 1bqi 1cvz 1eff 1khp 1khq 1pad 1pe6 1pip 1pop 1ppd 1ppn 1ppp 1stf 2pad 3e1z 3ima 3lfy 3tnx 3usv 4kp9 4pad 4qrg 4qrv 4qrx 5pad 6pad 9pap

(-) Related Entries Specified in the PDB File

1bp4 USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S '-SUBSITES.
1bqi USE OF PAPAIN AS A MODEL FOR THE STRUCTURE-BASED DESIGN OF CATHEPSIN K INHIBITORS. CRYSTAL STRUCTURES OF TWO PAPAIN INHIBITOR COMPLEXES DEMONSTRATE BINDING TO S '-SUBSITES.
1cvz CRYSTAL STRUCTURE ANALYSIS OF PAPAIN WITH CLIK148(CATHEPSIN L SPECIFIC INHIBITOR)
1eff KNOWLEDGE BASED MODEL OF AN INHIBITOR BOUND TO A THIOL(CYSTEIN) PROTEASE, PAPAIN COMPLEXED WITH NAPQI
1khp MONOCLINIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX
1khq ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX
1pad PAPAIN -ACETYL-ALANYL-ALANYL- PHENYLALANYL- METHYLENYLALANYL DERIVATIVE OF CYSTEINE 25 (/ ACAAPACK)
1pe6 PAPAIN COMPLEX WITH E-64-C
1pip PAPAIN COMPLEX WITH SUCCINYL-GLN-VAL-VAL- ALA-ALA-P-NITROANILIDE
1pop PAPAIN COMPLEX WITH LEUPEPTIN (N-ACETYL-L- LEUCYL-L-LEUCYL-L-ARGININAL)
1ppd 2-HYDROXYETHYLTHIOPAPAIN - CRYSTAL FORM D
1ppn PAPAIN CYS-25 WITH BOUND ATOM
1ppp PAPAIN COMPLEX WITH E64-C (FORM II)
1stf PAPAIN (CYS 25 CARBOXYMETHYLATED) COMPLEXED WITH THE INHIBITOR STEFIN B (CYSTATIN B) MUTANT WITH CYS I 8 REPLACED BY SER (C( I 8)S)
2pad PAPAIN -CYSTEINYL DERIVATIVE OF CYSTEINE-25 (/PAPSSCYS)
4pad PAPAIN -TOSYL-METHYLENYLLYSYL DERIVATIVE OF CYSTEINE-25 (/TLCK)
5pad PAPAIN -BENZYLOXYCARBONYL-GLYCYL- PHENYLALANYL- METHYLENYLGLYCYL DERIVATIVE (/ZGPGCK)
6pad PAPAIN -BENZYLOXYCARBONYL- PHENYLALANYL- METHYLENYLALANYL DERIVATIVE (/ZPACK)
9pap PAPAIN CYS-25 OXIDIZED