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(-) Description

Title :  CRYSTAL STRUCTURE OF A PSYCHROPHILIC ALKALINE PROTEASE FROM PSEUDOMONAS TAC II 18
 
Authors :  N. Aghajari, R. Haser
Date :  24 Nov 00  (Deposition) - 14 Feb 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.96
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (3x)
Keywords :  Beta Jelly Roll, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Aghajari, F. Van Petegem, V. Villeret, J. P. Chessa, C. Gerday, R. Haser, J. Van Beeumen
Crystal Structures Of A Psychrophilic Metalloprotease Revea New Insights Into Catalysis By Cold-Adapted Proteases
Proteins V. 50 636 2003
PubMed-ID: 12577270  |  Reference-DOI: 10.1002/PROT.10264
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SERRALYSIN
    Chains: A
    EC Number: 3.4.24.40
    Organism Scientific: PSEUDOMONAS
    Organism Taxid: 286
    Strain: TAC II 18
    Synonym: CALCIUM AND ZINC DEPENDENT ALKALINE PROTEASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CA7Ligand/IonCALCIUM ION
2SO41Ligand/IonSULFATE ION
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2SO43Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:49 , ASN A:51 , ASP A:53 , VAL A:55 , ASN A:57 , ASP A:114BINDING SITE FOR RESIDUE CA A 700
2AC2SOFTWAREARG A:250 , ASP A:252 , THR A:254 , ASP A:282 , GLY A:284 , ASP A:287BINDING SITE FOR RESIDUE CA A 701
3AC3SOFTWAREGLY A:285 , ASP A:287 , THR A:324 , GLU A:326 , HOH A:836 , HOH A:837BINDING SITE FOR RESIDUE CA A 702
4AC4SOFTWAREGLY A:331 , GLY A:333 , ASP A:335 , GLY A:348 , ALA A:350 , ASP A:353BINDING SITE FOR RESIDUE CA A 703
5AC5SOFTWAREGLY A:349 , GLY A:351 , ASP A:353 , GLY A:366 , THR A:368 , ASP A:371BINDING SITE FOR RESIDUE CA A 704
6AC6SOFTWAREASN A:340 , ALA A:342 , ASN A:344 , GLY A:357 , GLY A:359 , ASP A:362BINDING SITE FOR RESIDUE CA A 705
7AC7SOFTWAREGLY A:358 , GLY A:360 , ASP A:362 , ASP A:380 , ASP A:387 , HOH A:853BINDING SITE FOR RESIDUE CA A 706
8AC8SOFTWAREARG A:139 , TRP A:210 , SER A:211 , LYS A:213 , ASN A:214 , HOH A:763 , HOH A:825 , HOH A:826 , HOH A:967 , HOH A:1022BINDING SITE FOR RESIDUE SO4 A 500
9AC9SOFTWAREHIS A:169 , HIS A:173 , HIS A:179 , HOH A:932BINDING SITE FOR RESIDUE ZN A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1G9K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1G9K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1G9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1G9K)

(-) Exons   (0, 0)

(no "Exon" information available for 1G9K)

(-) 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:455
 aligned with O69771_9PSED | O69771 from UniProtKB/TrEMBL  Length:480

    Alignment length:461
                                    29        39        49        59        69        79        89        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       379       389       399       409       419       429       439       449       459       469       479 
         O69771_9PSED    20 GTSSAFTQIDNFSHFYDRGEHLVNGKPSFTVDQVADQLTRSGASWHDLNNDGVINLTYTFLTAPPVGYASRGLGTFSQFSALQKEQAKLSLESWADVAKVTFTEGPAARGDDGHMTFANFSASNGGAAFAYLPNSSRKGESWYLINKDYQVNKTPGEGNYGRQTLTHEIGHTLGLSHPGDYNAGNGNPTYRDAVYAEDTRAYSVMSYWSEKNTGQVFTKTGEGAYASAPLLDDIAAVQKLYGANLETRADDTVYGFNSTADRDFYSATSSTDKLIFSVWDGGGNDTLDFSGFSQNQKINLTAGSFSDVGGMTGNVSIAQGVTIENAIGGSGNDLLIGNDAANVLKGGAGNDIIYGGGGADVLWGGTGSDTFVFGAVSDSTPKAADIIKDFQSGFDKIDLTAITKLGGLNFVDAFTGHAGDAIVSYHQASNAGSLQVDFSGQGVADFLVTTVGQVATYDIVA 480
               SCOP domains d1g9ka2 A:3-244 Metalloprotease                                                                                                                                                                                                                   d1g9ka1 A:245-463 Metalloprotease                                                                                                                                                                                           SCOP domains
               CATH domains 1g9kA01          1g9kA02 A:20-247 Collagenase (Catalytic Domain)                                                                                                                                                                                     1g9kA01 A:3-19,A:248-461 Alkaline Protease, subunit P, domain 1                                                                                                                                                       -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh......ee..ee..hhhhhhhhhh..............eeeeeee......hhhhhh...ee..hhhhhhhhhhhhhhhhh...eeeee.....-..eeeeeeee.hhhhh.eee.........eeeee.....hhhhh....hhhhhhhhhhhhhhhh.......-----..hhhhh...............hhhhhh...............hhhhhhhhhhhhh..........eeee.....hhh.ee........eee.......eee........eee.....ee........eee.......eee......eee......eee......eee......eee......eee..hhhhh.....eee........eeehhhhhh....ee.........eeeeeee....eeeeeee........eeeeee...hhh.ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g9k A   3 GTSSAFTQIDNFSHFYDRGDHLVNGKPSFTVDQVADQLTRSGASWHDLNNDGVINLTYTFLTAPPVGYASRGLGTFSQFSALQKEQAKLSLESWADVAKVTFTEGPAAR-DDGHMTFANFSASNGGAAFAYLPNSSRKGESWYLINKDYQVNKTPGEGNYGRQTLTHEIGHTLGLSHPGDY-----NPTYRDAVYAEDTRAYSVMSYWSEKNTGQVFTKTGEGAYASAPLLDDIAAVQKLYGANLETRADDTVYGFNSTADRDFYSATSSTDKLIFSVWDGGGNDTLDFSGFSQNQKINLTAGSFSDVGGMTGNVSIAQGVTIENAIGGSGNDLLIGNDAANVLKGGAGNDIIYGGGGADVLWGGTGSDTFVFGAVSDSTPKAADIIKDFQSGFDKIDLTAITKLGGLNFVDAFTGHAGDAIVSYHQASNAGSLQVDFSGQGVADFLVTTVGQVATYDIVA 463
                                    12        22        32        42        52        62        72        82        92       102        |-|      122       132       142       152       162       172       182|     |192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462 
                                                                                                                                      111 |                                                                   183   189                                                                                                                                                                                                                                                                                  
                                                                                                                                        113
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1G9K)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (O69771_9PSED | O69771)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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: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: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: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: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)

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        O69771_9PSED | O69771: 1h71 1o0q 1o0t 1om6 1om7 1om8 1omj

(-) Related Entries Specified in the PDB File

1kap MESOPHILIC ALKALINE PROTEASE FROM PSEUDOMONAS AERUGINOSA
1sat METALLO PROTEASE FROM SERRATIA MARCESCENS