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(-) Description

Title :  PRO REGION OF ALPHA-LYTIC PROTEASE
 
Authors :  N. K. Sauter, T. Mau, S. D. Rader, D. A. Agard
Date :  20 Aug 98  (Deposition) - 27 Apr 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x)
Keywords :  Pro Region, Foldase, Protein Folding, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Sauter, T. Mau, S. D. Rader, D. A. Agard
Structure Of Alpha-Lytic Protease Complexed With Its Pro Region.
Nat. Struct. Biol. V. 5 945 1998
PubMed-ID: 9808037  |  Reference-DOI: 10.1038/2919
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-LYTIC PROTEASE
    Cell Line: B834
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: INCLUSION BODIES
    Expression System Plasmid: PT7PRO
    Expression System Strain: B834 (DE3) PLYSS
    Expression System Taxid: 562
    Fragment: PRO REGION
    Organism Scientific: LYSOBACTER ENZYMOGENES
    Organism Taxid: 69
    Other Details: T7 EXPRESSION SYSTEM

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C
Biological Unit 4 (1x): A (1x)B (1x)C (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PRO)

(-) Sites  (0, 0)

(no "Site" information available for 2PRO)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PRO)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PRO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PRO)

(-) 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:142
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:154
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187    
           PRLA_LYSEN    38 DPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGANARVKGVSKPLDGVQSWYVDPRSNAVVVKVDDGATEAGVDFVALSGADSAQVRIES 191
               SCOP domains d2proa1 A:5-85 Alpha-lytic protease prodomain                                    d2proa2 A:86-158             Alpha-lytic protease prodomain               SCOP domains
               CATH domains -2proA01 A:6-84  [code=3.30.300.50, no name defined]                            2proA02 A:85-157              [code=3.30.300.50, no name defined]        - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee............eeee....hhhhhhhhhhhhh..------------....eeee....eeee......hhhhhhhhhhh...hhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pro A   5 DPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGA------------GVQSWYVDPRSNAVVVKVDDGATDAGVDFVALSGADSAQVRIES 158
                                    14        24        34        44        54        64        74        84        94       | -         -|      124       134       144       154    
                                                                                                                           102          115                                           


Chain B from PDB  Type:PROTEIN  Length:143
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:155
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186     
           PRLA_LYSEN    37 VDPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGANARVKGVSKPLDGVQSWYVDPRSNAVVVKVDDGATEAGVDFVALSGADSAQVRIES 191
               SCOP domains d2prob1 B:4-85 Alpha-lytic protease prodomain                                     d2prob2 B:86-158             Alpha-lytic protease prodomain               SCOP domains
               CATH domains ---2proB01 B:7-84  [code=3.30.300.50, no name defined]                           2proB02 B:85-157              [code=3.30.300.50, no name defined]        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhheeeeeeee.....eeeeeee...........eeeee....hhhhhhhhhhhhhh.------------......................hhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pro B   4 VDPQLKFAMQRDLGIFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGA------------GVQSWYVDPRSNAVVVKVDDGATDAGVDFVALSGADSAQVRIES 158
                                    13        23        33        43        53        63        73        83        93        |-         - |     123       133       143       153     
                                                                                                                            102          115                                           


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with PRLA_LYSEN | P00778 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:141
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190 
           PRLA_LYSEN    51 IFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGANARVKGVSKPLDGVQSWYVDPRSNAVVVKVDDGATEAGVDFVALSGADSAQVRIES 191
               SCOP domains d2proc1 C:18-85 Alpha-lytic protease prodomain                      d2proc2 C:86-158             Alpha-lytic protease prodomain               SCOP domains
               CATH domains 2proC01 C:18-84  [code=3.30.300.50, no name defined]               2proC02 C:85-157              [code=3.30.300.50, no name defined]        - CATH domains
           Pfam domains (1) --------------------------------------------------------------------Pro_Al_protease-2            proC01 C:86-155                          --- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------Pro_Al_protease-2            proC02 C:86-155                          --- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------Pro_Al_protease-2            proC03 C:86-155                          --- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------Pro_Al_protease-2            proC04 C:86-155                          --- Pfam domains (4)
           Pfam domains (5) --------------------------------------------------------------------Pro_Al_protease-2            proC05 C:86-155                          --- Pfam domains (5)
           Pfam domains (6) --------------------------------------------------------------------Pro_Al_protease-2            proC06 C:86-155                          --- Pfam domains (6)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee.......eeeeee............eeee....hhhhhhhhhhhhhh.------------........hhh...........hhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pro C  18 IFPTQLPQYLQTEKLARTQAAAIEREFGAQFAGSWIERNEDGSFKLVAATSGARKSSTLGGVEVRNVRYSLKQLQSAMEQLDAGA------------GVQSWYVDPRSNAVVVKVDDGATDAGVDFVALSGADSAQVRIES 158
                                    27        37        47        57        67        77        87        97    |    -       117       127       137       147       157 
                                                                                                              102          115
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: Pro_Al_protease] (2)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (PRLA_LYSEN | P00778)
molecular function
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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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  2pro
    Family and Domain Information: ProDom | SYSTERS
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 Related Entries

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

UniProtKB/Swiss-Prot
        PRLA_LYSEN | P00778: 1boq 1gba 1gbb 1gbc 1gbd 1gbe 1gbf 1gbh 1gbi 1gbj 1gbk 1gbl 1gbm 1p01 1p02 1p03 1p04 1p05 1p06 1p09 1p10 1p11 1p12 1qq4 1qrw 1qrx 1ssx 1tal 2alp 2h5c 2h5d 2lpr 2ull 3lpr 3m7t 3m7u 3pro 3qgj 3urc 3urd 3ure 4pro 5lpr 6lpr 7lpr 8lpr 9lpr

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PRO)