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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL GERMINATION PROTEASE FROM SPORES OF BACILLUS MEGATERIUM: STRUCTURAL REARRANGEMENTS AND ZYMOGEN ACTIVATION
 
Authors :  K. Ponnuraj, S. Rowland, C. Nessi, P. Setlow, M. J. Jedrzejas
Date :  03 May 00  (Deposition) - 03 May 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Novel Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ponnuraj, S. Rowland, C. Nessi, P. Setlow, M. J. Jedrzejas
Crystal Structure Of A Novel Germination Protease From Spores Of Bacillus Megaterium: Structural Arrangement And Zymogen Activation.
J. Mol. Biol. V. 300 1 2000
PubMed-ID: 10864493  |  Reference-DOI: 10.1006/JMBI.2000.3849

(-) Compounds

Molecule 1 - SPORE PROTEASE
    Chains: A, B
    EC Number: 3.4.99.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BACILLUS MEGATERIUM
    Organism Taxid: 1404
    Other Details: ESCHERICHIA COLI
    Synonym: GERMINATION PROTEASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1C8B)

(-) Sites  (0, 0)

(no "Site" information available for 1C8B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C8B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1C8B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C8B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C8B)

(-) Exons   (0, 0)

(no "Exon" information available for 1C8B)

(-) 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:320
 aligned with GPR_BACMQ | P22321 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:371
                                                                                                                     90                                                                                                                                                                                                                                                                                        
                                                                                                                   89 |                                                                                                                                                                                                                                                                                        
                                    10        20        30        40        50        60        70        80        |-|       99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369 
            GPR_BACMQ     1 MEKELDLSQYSVRTDLAVEAKDIALENQPKPNNQSEIKGVIVKEKEEQGVKISMVEITEEGAEAIGKKKGRYVTLESVGIREQDTEKQE-AMEEVFAKELNFFIKSLNIPDDASCLVVGLGNLSVTPDALGPKAVDNLLITRHLFELQPESVQDGFRPVSAIVPGVMGMTGIETSDIIFGVVKKVNPDFIIAIDALAARSIERVNATIQISDSGIHPGSGVGNKRKEISYETLGIPVIAIGIPTVVDAVSITSDTIDFILKHFGREMKEQGKPSKSLLPSGMTFGEKKKLTEDDLPNEEQRQTYLGMIGTLPDEEKRRLIHEVLAPLGHNLMVTPKEVDMFIEDMANVVAGGLNAALHHEVDQENFGAYTH 370
               SCOP domains d1c8ba_ A: Germination proteas         e                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1c8bA00 A:401-771 HybD-like                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhh..---------....eeeeeeee..eeeeeeeehhhhhh......eeeeeee........hhhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhh...hhhhhhhh..........eeee.hhhhh....hhhhhhhhhhhhhh..eeeeeeee...hhhhh..eeeee......................---------...eeeeeee..ee...hhhhhh......---------------------------------..........hhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c8b A 401 MEKELDLSQYSVRTDLAVEAKDIALENQPK---------VIVKEKEEQGVKISMVEITEEGAEAIGKKKGRYVTLESVGIREQDTEKQEEAMEEVFAKELNFFIKSLNIPDDASCLVVGLGNLSVTPDALGPKAVDNLLITRHLFELQPESVQDGFRPVSAIVPGVMGMTGIETSDIIFGVVKKVNPDFIIAIDALAARSIERVNATIQISDSGIHPGSGVGNKRKEISYETL---------PTVVDAVSITSDTIDFILKHFGREMKEQG---------------------------------LGMIGTLPDEEKRRLIHEVLAPLGHNLMVTPKEVDMFIEDMANVVAGGLNAALHHEVDQENFGAYTH 771
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630  |      -  |    650       660       670|        -         -         -    |  710       720       730       740       750       760       770 
                                                       430       440                                                                                                                                                                                              633       643                         671                               705                                                                  


Chain B from PDB  Type:PROTEIN  Length:320
 aligned with GPR_BACMQ | P22321 from UniProtKB/Swiss-Prot  Length:370

    Alignment length:371
                                                                                                                     90                                                                                                                                                                                                                                                                                        
                                                                                                                   89 |                                                                                                                                                                                                                                                                                        
                                    10        20        30        40        50        60        70        80        |-|       99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369 
            GPR_BACMQ     1 MEKELDLSQYSVRTDLAVEAKDIALENQPKPNNQSEIKGVIVKEKEEQGVKISMVEITEEGAEAIGKKKGRYVTLESVGIREQDTEKQE-AMEEVFAKELNFFIKSLNIPDDASCLVVGLGNLSVTPDALGPKAVDNLLITRHLFELQPESVQDGFRPVSAIVPGVMGMTGIETSDIIFGVVKKVNPDFIIAIDALAARSIERVNATIQISDSGIHPGSGVGNKRKEISYETLGIPVIAIGIPTVVDAVSITSDTIDFILKHFGREMKEQGKPSKSLLPSGMTFGEKKKLTEDDLPNEEQRQTYLGMIGTLPDEEKRRLIHEVLAPLGHNLMVTPKEVDMFIEDMANVVAGGLNAALHHEVDQENFGAYTH 370
               SCOP domains d1c8bb_ B: Germination proteas         e                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1c8bB00 B:401-771 HybD-like                                                                                                                                                                                                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhh..---------.....eeeeeee..eeeeeee.hhhhhh.......eeeeee........hhhhhhhhhhhhhhhhhhh.......eeeee.....hhhhhhhhhhhhh...hhhhhhhh..........eeee.hhhhh....hhhhhhhhhhhhhh..eeeeeeee...hhhhh..eeeee......................---------...eeeeeee..ee...hhhhhh......---------------------------------..........hhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1c8b B 401 MEKELDLSQYSVRTDLAVEAKDIALENQPK---------VIVKEKEEQGVKISMVEITEEGAEAIGKKKGRYVTLESVGIREQDTEKQEEAMEEVFAKELNFFIKSLNIPDDASCLVVGLGNLSVTPDALGPKAVDNLLITRHLFELQPESVQDGFRPVSAIVPGVMGMTGIETSDIIFGVVKKVNPDFIIAIDALAARSIERVNATIQISDSGIHPGSGVGNKRKEISYETL---------PTVVDAVSITSDTIDFILKHFGREMKEQG---------------------------------LGMIGTLPDEEKRRLIHEVLAPLGHNLMVTPKEVDMFIEDMANVVAGGLNAALHHEVDQENFGAYTH 771
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630  |      -  |    650       660       670|        -         -         -    |  710       720       730       740       750       760       770 
                                                       430       440                                                                                                                                                                                              633       643                         671                               705
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C8B)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GPR_BACMQ | P22321)
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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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: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.
    GO:0009847    spore germination    The physiological and developmental changes that occur in a spore following release from dormancy up to the earliest signs of growth (e.g. emergence from a spore wall).

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