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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF THE ALKALINE PROTEASE OF PSEUDOMONAS AERUGINOSA: A TWO-DOMAIN PROTEIN WITH A CALCIUM BINDING PARALLEL BETA ROLL MOTIF
 
Authors :  U. Baumann, S. Wu, K. M. Flaherty, D. B. Mckay
Date :  08 Jun 95  (Deposition) - 15 Oct 95  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  I,P
Keywords :  Calcium Binding Protein, Zinc Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Baumann, S. Wu, K. M. Flaherty, D. B. Mckay
Three-Dimensional Structure Of The Alkaline Protease Of Pseudomonas Aeruginosa: A Two-Domain Protein With A Calcium Binding Parallel Beta Roll Motif.
Embo J. V. 12 3357 1993
PubMed-ID: 8253063

(-) Compounds

Molecule 1 - ALKALINE PROTEASE
    Chains: P
    EC Number: 3.4.24.-
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1
    Synonym: P. AERUGINOSA ALKALINE PROTEASE
 
Molecule 2 - TETRAPEPTIDE (GLY SER ASN SER)
    Chains: I
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 208964
    Strain: PAO1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : IP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1CA8Ligand/IonCALCIUM ION
2ZN1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER I:754 , HIS P:176 , HIS P:180 , HIS P:186BINDING SITE FOR RESIDUE ZN P 613
2AC2SOFTWAREARG P:253 , GLY P:255 , THR P:257 , ASP P:285 , GLY P:287 , ASP P:290BINDING SITE FOR RESIDUE CA P 614
3AC3SOFTWAREGLY P:288 , ASP P:290 , THR P:327 , GLU P:329 , HOH P:538 , HOH P:591BINDING SITE FOR RESIDUE CA P 615
4AC4SOFTWAREGLY P:334 , GLY P:336 , ASP P:338 , GLY P:351 , ALA P:353 , ASP P:356BINDING SITE FOR RESIDUE CA P 616
5AC5SOFTWAREGLY P:370 , GLY P:372 , ASP P:374 , ASP P:400 , HOH P:548 , HOH P:608BINDING SITE FOR RESIDUE CA P 617
6AC6SOFTWAREASN P:343 , VAL P:345 , ASN P:347 , GLY P:360 , LEU P:362 , ASP P:365BINDING SITE FOR RESIDUE CA P 618
7AC7SOFTWAREGLY P:361 , GLY P:363 , ASP P:365 , GLU P:383 , ASP P:390 , HOH P:544BINDING SITE FOR RESIDUE CA P 619
8AC8SOFTWAREGLY P:352 , GLY P:354 , ASP P:356 , GLY P:369 , ALA P:371 , ASP P:374BINDING SITE FOR RESIDUE CA P 620
9AC9SOFTWAREASP P:446 , SER P:448 , ASP P:450 , HIS P:452 , ASP P:454 , HOH P:692BINDING SITE FOR RESIDUE CA P 621

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric/Biological Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_APRA_PSEAE_001 *D127HAPRA_PSEAE  ---  ---PD118H
2UniProtVAR_APRA_PSEAE_002 *G176AAPRA_PSEAE  ---  ---PG167A
3UniProtVAR_APRA_PSEAE_003 *I350YAPRA_PSEAE  ---  ---PI341Y
4UniProtVAR_APRA_PSEAE_004 *I454VAPRA_PSEAE  ---  ---PI445V
5UniProtVAR_APRA_PSEAE_005 *A460RAPRA_PSEAE  ---  ---PA451R
6UniProtVAR_APRA_PSEAE_006 *V479LAPRA_PSEAE  ---  ---PV470L
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.APRA_PSEAE182-191  1P:173-182
2HEMOLYSIN_CALCIUMPS00330 Hemolysin-type calcium-binding region signature.APRA_PSEAE365-383  1P:356-374

(-) Exons   (0, 0)

(no "Exon" information available for 1KAP)

(-) Sequences/Alignments

Asymmetric/Biological 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 I from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1kap I 751 GSNS 754


Chain P from PDB  Type:PROTEIN  Length:470
 aligned with APRA_PSEAE | Q03023 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:470
                                    19        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
           APRA_PSEAE    10 GRSDAYTQVDNFLHAYARGGDELVNGHPSYTVDQAAEQILREQASWQKAPGDSVLTLSYSFLTKPNDFFNTPWKYVSDIYSLGKFSAFSAQQQAQAKLSLQSWSDVTNIHFVDAGQGDQGDLTFGNFSSSVGGAAFAFLPDVPDALKGQSWYLINSSYSANVNPANGNYGRQTLTHEIGHTLGLSHPGDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGAYSSAPLLDDIAAIQKLYGANLTTRTGDTVYGFNSNTERDFYSATSSSSKLVFSVWDAGGNDTLDFSGFSQNQKINLNEKALSDVGGLKGNVSIAAGVTVENAIGGSGSDLLIGNDVANVLKGGAGNDILYGGLGADQLWGGAGADTFVYGDIAESSAAAPDTLRDFVSGQDKIDLSGLDAFVNGGLVLQYVDAFAGKAGQAILSYDAASKAGSLAIDFSGDAHADFAINLIGQATQADIVV 479
               SCOP domains d1kapp2 P:1-246 Metalloprotease                                                                                                                                                                                                                       d1kapp1 P:247-470 Metalloprotease                                                                                                                                                                                                SCOP domains
               CATH domains 1kapP01          1kapP02 P:18-250 Collagenase (Catalytic Domain)                                                                                                                                                                                          1kapP01 P:1-17,P:251-470 Alkaline Protease, subunit P, domain 1                                                                                                                                                              CATH domains
           Pfam domains (1) --------------------------------------------------------------Reprolysin_2-1kapP01 P:63-231                                                                                                                                            -------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1k---------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1k---------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------HemolysinCabind-1k---------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Peptidase_M10_C-1kapP05 P:248-470                                                                                                                                                                                               Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhh.................hhhhhhhh...............eeeeeee.....hhhh.hhh...............hhhhhhhhhhhhhhh....eeeee........eeeeee.......eee...........eeeee...............hhhhhhhhhhhhhh................hhh.................hhhh.............hhhhhhhhhhh...........eee.......hhh..........eee.......eee........eee...............eee.......eee......eee......eee......eee......eee......eee...hhhh.....eee........eee....hhhh.................eeeeeee....eeeeeee........eeeeee....hhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------H------------------------------------------------A-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-------------------------------------------------------------------------------------------------------V-----R------------------L SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEMOLYSIN_CALCIUM  ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kap P   1 GRSDAYTQVDNFLHAYARGGDELVNGHPSYTVDQAAEQILREQASWQKAPGDSVLTLSYSFLTKPNDFFNTPWKYVSDIYSLGKFSAFSAQQQAQAKLSLQSWSDVTNIHFVDAGQGDQGDLTFGNFSSSVGGAAFAFLPDVPDALKGQSWYLINSSYSANVNPANGNYGRQTLTHEIGHTLGLSHPGDYNAGEGDPTYADATYAEDTRAYSVMSYWEEQNTGQDFKGAYSSAPLLDDIAAIQKLYGANLTTRTGDTVYGFNSNTERDFYSATSSSSKLVFSVWDAGGNDTLDFSGFSQNQKINLNEKALSDVGGLKGNVSIAAGVTVENAIGGSGSDLLIGNDVANVLKGGAGNDILYGGLGADQLWGGAGADTFVYGDIAESSAAAPDTLRDFVSGQDKIDLSGLDAFVNGGLVLQYVDAFAGKAGQAILSYDAASKAGSLAIDFSGDAHADFAINLIGQATQADIVV 470
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_MA (251)
(-)
Clan: no clan defined [family: HemolysinCabind] (16)
(-)
Clan: no clan defined [family: Peptidase_M10_C] (10)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (APRA_PSEAE | Q03023)
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: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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0045959    negative regulation of complement activation, classical pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation by the classical pathway.
    GO:0001869    negative regulation of complement activation, lectin pathway    Any process that stops, prevents, or reduces the rate of complement activation by the lectin pathway.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0010765    positive regulation of sodium ion transport    Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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.
    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)

UniProtKB/Swiss-Prot
        APRA_PSEAE | Q03023: 1akl 1jiw 3vi1

(-) Related Entries Specified in the PDB File

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