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(-) Description

Title :  CRYSTAL STRUCTURE OF NOCARDIOPSIS PROTEASE (NAPASE)
 
Authors :  B. A. Kelch, D. A. Agard
Date :  09 Feb 07  (Deposition) - 20 Feb 07  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serine Protease; Kinetic Stability; Acid Stability; Electrostatics, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Kelch, K. P. Eagen, F. P. Erciyas, E. L. Humphris, A. R. Thomason, S. Mitsuiki, D. A. Agard
Structural And Mechanistic Exploration Of Acid Resistance: Kinetic Stability Facilitates Evolution Of Extremophilic Behavior
J. Mol. Biol. V. 368 870 2007
PubMed-ID: 17382344  |  Reference-DOI: 10.1016/J.JMB.2007.02.032

(-) Compounds

Molecule 1 - SERINE PROTEASE
    Chains: A, B
    Organism Scientific: NOCARDIOPSIS ALBA
    Organism Taxid: 53437
    Other Details: GENE NAPA
    Secretion: YES
    Strain: TOA-1
    Synonym: PROTEIN NAPA

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1AES2Ligand/Ion4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2DIO3Ligand/Ion1,4-DIETHYLENE DIOXIDE
3GOL3Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (4, 7)
No.NameCountTypeFull Name
1AES1Ligand/Ion4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
3GOL2Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1AES1Ligand/Ion4-(2-AMINOETHYL)BENZENESULFONYL FLUORIDE
2DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE
3GOL1Ligand/IonGLYCEROL
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:9536 , HOH A:9577 , GLN B:62 , ARG B:85 , HOH B:9068BINDING SITE FOR RESIDUE SO4 A 9400
02AC2SOFTWAREPRO A:131 , ILE A:132 , ARG A:165 , HOH A:9419 , HOH A:9530 , HOH A:9596BINDING SITE FOR RESIDUE SO4 A 9401
03AC3SOFTWAREGLU A:191 , ASP A:194 , SER A:195 , THR A:213 , SER A:214 , GLY A:215 , GLY A:216 , HOH A:9430BINDING SITE FOR RESIDUE AES A 9001
04AC4SOFTWAREALA B:190 , GLU B:191 , SER B:195 , THR B:213 , SER B:214 , GLY B:215 , GLY B:216 , HOH B:9036 , HOH B:9142BINDING SITE FOR RESIDUE AES B 9002
05AC5SOFTWAREASN A:101 , ALA A:103 , SER A:237 , TRP A:238BINDING SITE FOR RESIDUE DIO A 9003
06AC6SOFTWARELEU A:120A , ASN B:101 , PRO B:233 , MET B:234 , TRP B:238BINDING SITE FOR RESIDUE DIO A 9004
07AC7SOFTWARECYS B:219A , ARG B:220 , THR B:222 , GLY B:223BINDING SITE FOR RESIDUE DIO B 9005
08AC8SOFTWAREASN B:48A , ALA B:48B , GLU B:88A , ARG B:89 , TRP B:238 , HOH B:9084BINDING SITE FOR RESIDUE GOL B 9006
09AC9SOFTWARELEU A:120A , TYR A:120J , HOH A:9477 , VAL B:59B , ARG B:89 , SER B:90 , TRP B:238 , HOH B:9033 , HOH B:9163BINDING SITE FOR RESIDUE GOL A 9007
10BC1SOFTWARELEU A:114 , THR A:119 , ARG A:243 , THR A:244 , HOH A:9472 , HOH A:9525 , ASN B:236 , SER B:237 , ASN B:239BINDING SITE FOR RESIDUE GOL A 9009

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:42 -A:58
2A:137 -A:159
3A:189 -A:219A
4B:42 -B:58
5B:137 -B:159
6B:189 -B:219A

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:94 -Pro A:95
2Phe B:94 -Pro B:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2OUA)

(-) 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:188
 aligned with Q6K1C5_9ACTN | Q6K1C5 from UniProtKB/TrEMBL  Length:384

    Alignment length:188
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376        
        Q6K1C5_9ACTN    197 ADIIGGLAYTMGGRCSVGFAATNASGQPGFVTAGHCGSVGTQVSIGNGRGVFERSVFPGNDAAFVRGTSNFTLTNLVSRYNSGGYATVSGSSTAPIGSQVCRSGSTTGWYCGTIQARNQTVSYPQGTVHSLTRTSVCAEPGDSAGSFISGTQAQGVTSGGSGNCRTGGTTFYQEVNPMLNSWNLRLRT  384
               SCOP domains d2ouaa_ A: automated matches                                                                                                                                                                 SCOP domains
               CATH domains 2ouaA01 A:15A-119,A:231-244 Trypsin-like serine proteases                 2ouaA02 A:120-230 Trypsin-like serine proteases                                                     2ouaA01        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee...eee..eeee.....eeeeehhhhh....eeee..eeeeeeeee.....eeeeeeee..eeeeeee.hhhh.eee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeeeeee...eeeeeeeehhhhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2oua A  15A ADIIGGLAYTMGGRCSVGFAATNASGQPGFVTAGHCGSVGTQVSIGNGRGVFERSVFPGNDAAFVRGTSNFTLTNLVSRYNSGGYATVSGSSTAPIGSQVCRSGSTTGWYCGTIQARNQTVSYPQGTVHSLTRTSVCAEPGDSGGSFISGTQAQGVTSGGSGNCRTGGTTFYQEVNPMLNSWNLRLRT  244
                            ||   || 36  ||   |46  ||||  52       |60 ||  || 86  |  ||101       111  || |120E|||||||123 ||    136      |158       168  ||   179     ||192      201A|      216   ||| 226       236        
                            ||  19|    39| 44A  48A|||         59A| 62| 67|   88A 91|||           114| ||||120H||||  125|           143|            171|         185|         201A|         219A||                      
                          15A|   33     41       48B||          59B  64  83        94||            119 |||||120I|||   129            156             173          189           207           220|                      
                           15B                    48C|                              95|             120A|||||120J||                                                                            222                      
                                                   48D                              100              120B|||||120K|                                                                                                     
                                                                                                      120C|||| 120L                                                                                                     
                                                                                                       120D|||                                                                                                          
                                                                                                        120E||                                                                                                          
                                                                                                         120F|                                                                                                          
                                                                                                          120G                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:188
 aligned with Q6K1C5_9ACTN | Q6K1C5 from UniProtKB/TrEMBL  Length:384

    Alignment length:188
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376        
        Q6K1C5_9ACTN    197 ADIIGGLAYTMGGRCSVGFAATNASGQPGFVTAGHCGSVGTQVSIGNGRGVFERSVFPGNDAAFVRGTSNFTLTNLVSRYNSGGYATVSGSSTAPIGSQVCRSGSTTGWYCGTIQARNQTVSYPQGTVHSLTRTSVCAEPGDSAGSFISGTQAQGVTSGGSGNCRTGGTTFYQEVNPMLNSWNLRLRT  384
               SCOP domains d2ouab_ B: automated matches                                                                                                                                                                 SCOP domains
               CATH domains 2ouaB01 B:15A-119,B:231-244 Trypsin-like serine proteases                 2ouaB02 B:120-230 Trypsin-like serine proteases                                                     2ouaB01        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee...eee..eeee.....eeeeehhhhh....eeee..eeeeeeeee.....eeeeeeee..eeeeeee.hhhh.eee...........eeeeee...eeeeeeeeeeeeeeee..eeeeeeeee...........eeee..eeeeeeeeeeee...eeeeeeeehhhhhhhh..ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2oua B  15A ADIIGGLAYTMGGRCSVGFAATNASGQPGFVTAGHCGSVGTQVSIGNGRGVFERSVFPGNDAAFVRGTSNFTLTNLVSRYNSGGYATVSGSSTAPIGSQVCRSGSTTGWYCGTIQARNQTVSYPQGTVHSLTRTSVCAEPGDSGGSFISGTQAQGVTSGGSGNCRTGGTTFYQEVNPMLNSWNLRLRT  244
                            ||   || 36  ||   |46  ||||  52       |60 ||  || 86  |  ||101       111  || |120E|||||||123 ||    136      |158       168  ||   179     ||192      201A|      216   ||| 226       236        
                          15A|  19|    39| 44A  48A|||         59A| 62| 67|   88A 91|||           114| ||||120H||||  125|           143|            171|         185|         201A|         219A||                      
                           15B   33     41       48B||          59B  64  83        94||            119 |||||120I|||   129            156             173          189           207           220|                      
                                                  48C|                              95|             120A|||||120J||                                                                            222                      
                                                   48D                              100              120B|||||120K|                                                                                                     
                                                                                                      120C|||| 120L                                                                                                     
                                                                                                       120D|||                                                                                                          
                                                                                                        120E||                                                                                                          
                                                                                                         120F|                                                                                                          
                                                                                                          120G
   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: All beta proteins (24004)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2OUA)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6K1C5_9ACTN | Q6K1C5)
molecular function
    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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