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(-) Description

Title :  STRUCTURE OF GLU ENDOPEPTIDASE IN COMPLEX WITH MPD
 
Authors :  R. Meijers, E. V. Blagova, V. M. Levdikov, G. N. Rudenskaya, G. G. Chestu T. V. Akimkina, S. V. Kostrov, V. S. Lamzin, I. P. Kuranova
Date :  17 Apr 03  (Deposition) - 27 Apr 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Serine Protease, Glu Specific, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Meijers, E. V. Blagova, V. M. Levdikov, G. N. Rudenskaya, G. G. Chestukhina, T. V. Akimkina, S. V. Kostrov, V. S. Lamzin, I. P. Kuranova
The Crystal Structure Of Glutamyl Endopeptidase From Bacillus Intermedius Reveals A Structural Link Between Zymogen Activation And Charge Compensation.
Biochemistry V. 43 2784 2004
PubMed-ID: 15005613  |  Reference-DOI: 10.1021/BI035354S

(-) Compounds

Molecule 1 - GLUTAMYL-ENDOPEPTIDASE
    Chains: A
    Organism Scientific: BACILLUS INTERMEDIUS
    Organism Taxid: 1400
    Strain: 3-19

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:1 , GLY A:29 , THR A:166 , PHE A:167 , SER A:168 , HIS A:186BINDING SITE FOR RESIDUE MPD A 300

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:32 -A:48

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:17 -Pro A:18

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P3E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P3E)

(-) Exons   (0, 0)

(no "Exon" information available for 1P3E)

(-) 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:215
 aligned with Q9EXR9_BACIN | Q9EXR9 from UniProtKB/TrEMBL  Length:303

    Alignment length:215
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     
         Q9EXR9_BACIN    89 VVIGDDGRTKVANTRVAPYNSIAYITFGGSSCTGTLIAPNKILTNGHCVYNTASRSYSAKGSVYPGMNDSTAVNGSANMTEFYVPSGYINTGASQYDFAVIKTDTNIGNTVGYRSIRQVTNLTGTTIKISGYPGDKMRSTGKVSQWEMSGSVTREDTNLAYYTIDTFSGNSGSAMLDQNQQIVGVHNAGYSNGTINGGPKATAAFVEFINYAKAQ 303
               SCOP domains d1p3ea_ A: Glutamyl endopeptidase                                                                                                                                                                                       SCOP domains
               CATH domains 1p3eA01          1p3eA02 A:18-115,A:203-215 Trypsin-like serine proteases                                          1p3eA01 A:1-17,A:116-202 Trypsin-like serine proteases                                 1p3eA02       CATH domains
               Pfam domains ------Trypsin-1p3eA01 A:7-213                                                                                                                                                                                        -- Pfam domains
         Sec.struct. author ........ee.......hhh.eeeee....eeeeeeee..eeeehhhhhee....ee....eeee...........eeeeeee.hhhhhhhhhhhhh.eeeee...hhhhhh.............eeeeee.hhhhhhhhh....eeeeee..ee...eeee...........eee.....eeee..eee....eeeee..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p3e A   1 VVIGDDGRTKVANTRVAPYNSIAYITFGGSSCTGTLIAPNKILTNGHCVYNTASRSYSAKGSVYPGMNDSTAVNGSANMTEFYVPSGYINTGASQYDFAVIKTDTNIGNTVGYRSIRQVTNLTGTTIKISGYPGDKMRSTGKVSQWEMSGSVTREDTNLAYYTIDTFSGNSGSAMLDQNQQIVGVHNAGYSNGTINGGPKATAAFVEFINYAKAQ 215
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Peptidase_PA (797)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9EXR9_BACIN | Q9EXR9)
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.

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 Related Entries

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        Q9EXR9_BACIN | Q9EXR9: 1p3c

(-) Related Entries Specified in the PDB File

1p3c