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(-) Description

Title :  THE REFINED 2.4 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF RECOMBINANT HUMAN STEFIN B IN COMPLEX WITH THE CYSTEINE PROTEINASE PAPAIN: A NOVEL TYPE OF PROTEINASE INHIBITOR INTERACTION
 
Authors :  M. T. Stubbs, B. Laber, W. Bode
Date :  21 Apr 93  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Hydrolase(Sulfhydryl Proteinase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. T. Stubbs, B. Laber, W. Bode, R. Huber, R. Jerala, B. Lenarcic, V. Turk
The Refined 2. 4 A X-Ray Crystal Structure Of Recombinant Human Stefin B In Complex With The Cysteine Proteinase Papain: A Novel Type Of Proteinase Inhibitor Interaction.
Embo J. V. 9 1939 1990
PubMed-ID: 2347312
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PAPAIN
    ChainsE
    EC Number3.4.22.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    OrganFRUIT
    Organism CommonPAPAYA
    Organism ScientificCARICA PAPAYA
    Organism Taxid3649
 
Molecule 2 - STEFIN B (CYSTATIN B)
    ChainsI
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    OrganFRUIT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit EI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CCS1Mod. Amino AcidCARBOXYMETHYLATED CYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 1STF)

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly E:151 -Pro E:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_002206G4RCYTB_HUMANDisease (EPM1)74315443IG9R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYSTATINPS00287 Cysteine proteases inhibitors signature.CYTB_HUMAN45-58  1I:52-65
2THIOL_PROTEASE_CYSPS00139 Eukaryotic thiol (cysteine) proteases cysteine active site.PAPA1_CARPA152-163  1E:19-30
3THIOL_PROTEASE_HISPS00639 Eukaryotic thiol (cysteine) proteases histidine active site.PAPA1_CARPA290-300  1E:157-167
4THIOL_PROTEASE_ASNPS00640 Eukaryotic thiol (cysteine) proteases asparagine active site.PAPA1_CARPA303-322  1E:170-189

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002915681aENSE00001137740chr21:45196326-45196085242CYTB_HUMAN1-22221I:6-2722
1.2aENST000002915682aENSE00001050609chr21:45194640-45194539102CYTB_HUMAN23-56341I:28-63 (gaps)36
1.2cENST000002915682cENSE00001957681chr21:45194211-451923931819CYTB_HUMAN57-98421I:64-125 (gaps)65

(-) 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: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 d1stfe_ E: Papain                                                                                                                                                                                                    SCOP domains
               CATH domains 1stfE00 E:1-212 Cysteine proteinases                                                                                                                                                                                 CATH domains
               Pfam domains Peptidase_C1-1stfE01 E:1-210                                                                                                                                                                                      -- Pfam domains
         Sec.struct. author ....eee................hhhhhhhhhhhhhhhhhhhh......hhhhhhhh.........hhhhhhhhhhhh.............................eeeeee...hhhhhhhhhhhh.eeeee...hhhhhh..............eeeeeeeeee..eeeeee.........eeeeeee..............eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------THIOL_PROTEA------------------------------------------------------------------------------------------------------------------------------THIOL_PROTE--THIOL_PROTEASE_ASN  ----------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1stf E    1 IPEYVDWRQKGAVTPVKNQGSCGScWAFSAVVTIEGIIKIRTGNLNQYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNQGALLYSIANQPVSVVLQAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN  212
                                    10        20    |   30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
                                                   25-CCS                                                                                                                                                                                       

Chain I from PDB  Type:PROTEIN  Length:98
 aligned with CYTB_HUMAN | P04080 from UniProtKB/Swiss-Prot  Length:98

    Alignment length:98
                                    10        20        30        40        50        60        70        80        90        
          CYTB_HUMAN      1 MMCGAPSATQPATAETQHIADQVRSQLEEKENKKFPVFKAVSFKSQVVAGTNYFIKVHVGDEDFVHLRVFQSLPHENKPLTLSNYQTNKAKHDELTYF   98
               SCOP domains d1stfi_ I: Cystatin B (stefin B)                                                                   SCOP domains
               CATH domains 1stfI00 I:6-125  [code=3.10.450.10, no name defined]                                               CATH domains
               Pfam domains ---Cystatin-1stfI01 I:9-119                                                                 ------ Pfam domains
         Sec.struct. author .................................................................................................. Sec.struct. author
                 SAPs(SNPs) ---R---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------CYSTATIN      ---------------------------------------- PROSITE
               Transcript 1 Exon 1.1a  PDB: I:6-27Exon 1.2a  PDB: I:28-63 (gaps)    Exon 1.2c  PDB: I:64-125 (gaps)            Transcript 1
                1stf I    6 MMSGAPSATQPATAETQHIADQVRSQLEEKYNKKFPVFKAVSFKSQVVAGTNYFIKVHVGDEDFVHLRVFQSLPHENKPLTLSNYQTNKAKHDELTYF  125
                                    15        25        35    ||  47        57        67||     100  |   |108       117        
                                                             40|                       68|       102A   |       115A          
                                                              43                        92           105A                     

   Legend:   → Mismatch (orange background)
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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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Cystatin (20)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (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 I   (CYTB_HUMAN | P04080)
molecular function
    GO:0004869    cysteine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of a cysteine-type endopeptidase, any enzyme that hydrolyzes peptide bonds in polypeptides by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0004866    endopeptidase inhibitor activity    Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
    GO:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
biological process
    GO:0008344    adult locomotory behavior    Locomotory behavior in a fully developed and mature organism.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0045861    negative regulation of proteolysis    Any process that stops, prevents, or reduces the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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  The papain-stefin B complex: ribbon representation (PDB code: 1stf) (mono).

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 Related Entries

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UniProtKB/Swiss-Prot
        CYTB_HUMAN | P040802oct 4n6v
        PAPA1_CARPA | P007841bp4 1bqi 1cvz 1eff 1khp 1khq 1pad 1pe6 1pip 1pop 1ppd 1ppn 1ppp 2cio 2pad 3e1z 3ima 3lfy 3tnx 3usv 4kp9 4pad 4qrg 4qrv 4qrx 5pad 6pad 9pap

(-) Related Entries Specified in the PDB File

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