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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF PORCINE PROCARBOXYPEPTIDASE B: A STRUCTURAL BASIS OF ITS INACTIVITY
 
Authors :  R. Huber
Date :  25 Jul 97  (Deposition) - 24 Dec 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Porcine Procarboxypeptidase, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Coll, A. Guasch, F. X. Aviles, R. Huber
Three-Dimensional Structure Of Porcine Procarboxypeptidase B: A Structural Basis Of Its Inactivity.
Embo J. V. 10 1 1991
PubMed-ID: 1989878
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROCARBOXYPEPTIDASE B
    Chains: A
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1BEN3Ligand/IonBENZAMIDINE
2ZN1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , HOH A:502BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREASN A:144 , SER A:207 , ALA A:250 , GLY A:253 , ASP A:255BINDING SITE FOR RESIDUE BEN A 1
3AC3SOFTWAREGLU A:20A , PRO A:48A , LEU A:62A , ALA A:63A , ASP A:66A , TYR A:248 , HOH A:581 , HOH A:610BINDING SITE FOR RESIDUE BEN A 2
4AC4SOFTWAREASP A:31 , TYR A:92 , TYR A:210 , HOH A:531 , HOH A:696 , HOH A:697BINDING SITE FOR RESIDUE BEN A 3

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:66 -A:79
2A:138 -A:161
3A:152 -A:166

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Lys A:39A-Pro A:40A
2Ser A:197 -Tyr A:198
3Pro A:205 -Tyr A:206
4Arg A:272 -Asp A:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPB1_PIG167-189  1A:60-82
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPB1_PIG304-314  1A:196-206

(-) Exons   (0, 0)

(no "Exon" information available for 1NSA)

(-) 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:395
 aligned with CBPB1_PIG | P09955 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:395
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     
           CBPB1_PIG     22 FEGEKVFRVNVEDENDISLLHELASTRQIDFWKPDSVTQIKPHSTVDFRVKAEDILAVEDFLEQNELQYEVLINNLRSVLEAQFDSRVRTTGHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  416
               SCOP domains d1nsaa2 A:7A-95A Procarboxypeptidase B                                                   d1nsaa1 A:4-308 Carboxypeptidase B                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1nsaA01 A:7A-6  [code=3.30.70.340, no name defined]                                         1nsaA02 A:7-308 Zn peptidases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------Propep_M14-1nsaA02 A:13A-90A                                                  -------------------Peptidase_M14-1nsaA01 A:18-296                                                                                                                                                                                                                                                          ------------ Pfam domains
         Sec.struct. author ....eeeeeee..hhhhhhhhhhhhh..eeeee...hhh....eeeeeee.hhhhhhhhhhhhhh..eeeeee..hhhhhhh..................hhhhhhhhhhhhhh....eeeee..........eeeee........eeeee........hhhhhhhhhhhhhhhh....hhhhhhhhh.eeeee....hhhhhhhhh.....................hhh............................hhhhhhhhhhhhh...eeeeee......eeee...........hhhhhhhhhhhhhhhhhhh....eeeehhhh.......hhhhhhhh...eeeeee............hhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1nsa A   7A FEGEKVFRVNVEDENDISELHELASTRQIDFWKPDSVTQIKPHSTVDFRVKAEDILAVEDFLEQNELQYEVLINNLRSVLEAQFDSVSRTTGHSYEKYNNWETIEAWTEQVTSKNPDLISRSAIGTTFDGDNIYLLKVGKPGSNKPAIFMDCGFHAREWISQAFCQWFVRDAVRTYGYEAHMTEFLDNLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGSSCTGTDPNRNFNAGWCTVGASVNPCNETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENDAELNSLAKGAVKELASLYGTSYSYGPGSTTIYPAAGGSDDWAYNQGIKYSFTFELRDKGRFGFVLPESQIQATCQETMLAVKYVTNYTLEHL  308
                            |||||||16A|||||||26A|||||||36A|||||||46A|||||||56A|||||||66A|||||||76A|||||||86A|||||||||4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184    |  193       203       213       223       233       243       253       263       273       283       293       303     
                            ||||||15A||||||24A||||||33A||||||42A||||||51A||||||60A||||||69A||||||78A||||||87A||||||||4                                                                                                                                                                                     188A                                                                                                                        
                           7A||||||16A||||||25A||||||34A||||||43A||||||52A||||||61A||||||70A||||||79A||||||88A|||||||                                                                                                                                                                                                                                                                                                                  
                            8A||||||17A||||||26A||||||35A||||||44A||||||53A||||||62A||||||71A||||||80A||||||89A||||||                                                                                                                                                                                                                                                                                                                  
                             9A||||| 18A||||| 27A||||| 36A||||| 45A||||| 54A||||| 63A||||| 72A||||| 81A||||| 90A|||||                                                                                                                                                                                                                                                                                                                  
                             10A||||  19A||||  28A||||  37A||||  46A||||  55A||||  64A||||  73A||||  82A||||  91A||||                                                                                                                                                                                                                                                                                                                  
                              11A|||   20A|||   29A|||   38A|||   47A|||   56A|||   65A|||   74A|||   83A|||   92A|||                                                                                                                                                                                                                                                                                                                  
                               12A||    21A||    30A||    39A||    48A||    57A||    66A||    75A||    84A||    93A||                                                                                                                                                                                                                                                                                                                  
                                13A|     22A|     31A|     40A|     49A|     58A|     67A|     76A|     85A|     94A|                                                                                                                                                                                                                                                                                                                  
                                 14A      23A      32A      41A      50A      59A      68A      77A      86A      95A
   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: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MH (119)
(-)
Clan: no clan defined [family: Propep_M14] (5)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPB1_PIG | P09955)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004181    metallocarboxypeptidase activity    Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBPB1_PIG | P09955: 1pba 1z5r 1zg7 1zg8 1zg9 2jew 2piy 2piz 2pj0 2pj1 2pj2 2pj3 2pj4 2pj5 2pj6 2pj7 2pj8 2pj9 2pja 2pjb 2pjc 3glj 3wab 3wc5 3wc6 3wc7 4uia 4uib 4z65 5j1q 5jc6 5lrg 5lrj 5lrk 5lyd 5lyf 5lyi 5lyl

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