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(-) Description

Title :  STRUCTURAL CHARACTERISTICS OF ALKALINE PHOSPHATASE FROM A MODERATELY HALOPHILIC BACTERIA HALOMONAS SP.593
 
Authors :  S. Arai, Y. Yonezawa, M. Ishibashi, F. Matsumoto, T. Tamada, H. Tokunag M. Tokunaga, R. Kuroki
Date :  17 May 13  (Deposition) - 12 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crown-Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Arai, Y. Yonezawa, M. Ishibashi, F. Matsumoto, M. Adachi, T. Tamada H. Tokunaga, M. Blaber, M. Tokunaga, R. Kuroki
Structural Characteristics Of Alkaline Phosphatase From The Moderately Halophilic Bacterium Halomonas Sp. 593.
Acta Crystallogr. , Sect. D V. 70 811 2014
PubMed: search  |  Reference-DOI: 10.1107/S1399004713033609

(-) Compounds

Molecule 1 - ALKALINE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21 STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: HALOMONAS
    Organism Taxid: 195704
    Strain: 593

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MG6Ligand/IonMAGNESIUM ION
3ZN4Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:12 , THR A:118 , GLU A:264 , HOH A:638 , HOH A:639 , HOH A:640BINDING SITE FOR RESIDUE MG A 501
02AC2SOFTWAREALA A:45 , LYS A:46 , GLY A:48 , SER B:481 , SER B:482 , HOH B:637BINDING SITE FOR RESIDUE MG A 502
03AC3SOFTWAREGLY A:103 , ASP A:255 , GLU A:256 , ASP A:257 , HOH A:634 , HOH A:646BINDING SITE FOR RESIDUE MG A 503
04AC4SOFTWAREASP A:269 , HIS A:273 , HIS A:461 , CL A:506 , HOH A:636 , HOH B:633BINDING SITE FOR RESIDUE ZN A 504
05AC5SOFTWAREASP A:12 , SER A:65 , ASP A:311 , HIS A:312BINDING SITE FOR RESIDUE ZN A 505
06AC6SOFTWARESER A:65 , ARG A:129 , ASP A:269 , HIS A:461 , ZN A:504 , HOH B:633BINDING SITE FOR RESIDUE CL A 506
07AC7SOFTWAREASP B:12 , THR B:118 , GLU B:264 , HOH B:635 , HOH B:636 , HOH B:638BINDING SITE FOR RESIDUE MG B 501
08AC8SOFTWARESER A:481 , SER A:482 , HOH A:623 , ALA B:45 , LYS B:46 , GLY B:48BINDING SITE FOR RESIDUE MG B 502
09AC9SOFTWAREGLY B:103 , ASP B:255 , ASP B:257 , HOH B:641 , HOH B:642BINDING SITE FOR RESIDUE MG B 503
10BC1SOFTWAREHOH A:637 , ASP B:269 , HIS B:273 , HIS B:461 , CL B:506 , HOH B:634BINDING SITE FOR RESIDUE ZN B 504
11BC2SOFTWAREASP B:12 , SER B:65 , ASP B:311 , HIS B:312BINDING SITE FOR RESIDUE ZN B 505
12BC3SOFTWAREHOH A:637 , SER B:65 , ARG B:129 , ASP B:269 , HIS B:461 , ZN B:504 , HOH B:634BINDING SITE FOR RESIDUE CL B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WBH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WBH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WBH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WBH)

(-) Exons   (0, 0)

(no "Exon" information available for 3WBH)

(-) 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 A from PDB  Type:PROTEIN  Length:497
 aligned with B5BP20_9GAMM | B5BP20 from UniProtKB/TrEMBL  Length:527

    Alignment length:497
                                    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       480       490       500       510       520       
         B5BP20_9GAMM    31 EVKNVILMIGDGMGPQQVGLLETYANQAPDSIYDGEPTAFHQLAKEGVVGFSLTHPEDAVVVDSACSATQLASGIYSGSEVIGIDAEGNPVETVLELAQARGKATGLVSDTRLTHATPAAFAAHQPHRSLENEIAVDMLEVGPDVMLSGGLRHWVPQSASEDAEVTSLMDGAYEPASKRQDDRNLLAEAVEKGYGLAFSREQLEADQSDKLLGLFANSGMADGIEYRNTRDDADRREPTLHEMTQAALNRLEQDEDGFFLMVEGGQIDWAGHSNDAGTMLNEMVKFEEAVQGVYDWAKGREDTVILVTADHETGAFGLSYSSADLPEPQSKSGPAFAERDYAPNFNFGDFALLDSLYHQKASFSTLLSEFGALEEEQRTPARLMEMVNANSDFQIDEEQAEAVLADKPNPYHVEGHSYLEAEEVPAIQDFDAFYPYNDRGNVLGRVLGTAQNVVWGTGTHTHTPVNVFAWGPAETILPVSSIQHHSEVGQYLKSLVE 527
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhhhhhhhhhh.........hhhhhhhhhheeeeee.........hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh.........hhhhhhhhhhhhh..eeeeehhhhh...hhhhhhhhhhhhh.............hhhhhhhhh..eee.hhhhhhhh....eeee.......hhhhhhhhh........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeee..eee..............hhhhh............hhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhheee..............eee....hhhhh...hhhhhhhhhhhhhhheee....ee...eeeeee.hhhhhhhhh.eeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wbh A   2 EVKNVILMIGDGMGPQQVGLLETYANQAPDSIYDGEPTAFHQLAKEGVVGFSLTHPEDAVVVDSACSATQLASGIYSGSEVIGIDAEGNPVETVLELAQARGKATGLVSDTRLTHATPAAFAAHQPHRSLENEIAVDMLEVGPDVMLSGGLRHWVPQSASEDAEVTSLMDGAYEPASKRQDDRNLLAEAVEKGYGLAFSREQLEADQSDKLLGLFANSGMADGIEYRNTRDDADRREPTLHEMTQAALNRLEQDEDGFFLMVEGGQIDWAGHSNDAGTMLNEMVKFEEAVQGVYDWAKGREDTVILVTADHETGAFGLSYSSADLPEPQSKSGPAFAERDYAPNFNFGDFALLDSLYHQKASFSTLLSEFGALEEEQRTPARLMEMVNANSDFQIDEEQAEAVLADKPNPYHVEGHSYLEAEEVPAIQDFDAFYPYNDRGNVLGRVLGTAQNVVWGTGTHTHTPVNVFAWGPAETILPVSSIQHHSEVGQYLKSLVE 498
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       


Chain B from PDB  Type:PROTEIN  Length:497
 aligned with B5BP20_9GAMM | B5BP20 from UniProtKB/TrEMBL  Length:527

    Alignment length:497
                                    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       480       490       500       510       520       
         B5BP20_9GAMM    31 EVKNVILMIGDGMGPQQVGLLETYANQAPDSIYDGEPTAFHQLAKEGVVGFSLTHPEDAVVVDSACSATQLASGIYSGSEVIGIDAEGNPVETVLELAQARGKATGLVSDTRLTHATPAAFAAHQPHRSLENEIAVDMLEVGPDVMLSGGLRHWVPQSASEDAEVTSLMDGAYEPASKRQDDRNLLAEAVEKGYGLAFSREQLEADQSDKLLGLFANSGMADGIEYRNTRDDADRREPTLHEMTQAALNRLEQDEDGFFLMVEGGQIDWAGHSNDAGTMLNEMVKFEEAVQGVYDWAKGREDTVILVTADHETGAFGLSYSSADLPEPQSKSGPAFAERDYAPNFNFGDFALLDSLYHQKASFSTLLSEFGALEEEQRTPARLMEMVNANSDFQIDEEQAEAVLADKPNPYHVEGHSYLEAEEVPAIQDFDAFYPYNDRGNVLGRVLGTAQNVVWGTGTHTHTPVNVFAWGPAETILPVSSIQHHSEVGQYLKSLVE 527
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhhhhhhhhhhh.........hhhhhhhhhheeeeee.........hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh.........hhhhhhhhhhhhh..eeeeehhhhh...hhhhhhhhhhhhh.............hhhhhhhhh..eee.hhhhhhhh....eeee.......hhhhhhhhh........hhhhhhhhhhhhhh.....eeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..ee...ee..............hhhhh............hhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhh....hhhhhhhhhheee..............eee....hhhhh...hhhhhhhhhhhhhhhee.....ee...eeeeee.hhhhhhhhh.eeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wbh B   2 EVKNVILMIGDGMGPQQVGLLETYANQAPDSIYDGEPTAFHQLAKEGVVGFSLTHPEDAVVVDSACSATQLASGIYSGSEVIGIDAEGNPVETVLELAQARGKATGLVSDTRLTHATPAAFAAHQPHRSLENEIAVDMLEVGPDVMLSGGLRHWVPQSASEDAEVTSLMDGAYEPASKRQDDRNLLAEAVEKGYGLAFSREQLEADQSDKLLGLFANSGMADGIEYRNTRDDADRREPTLHEMTQAALNRLEQDEDGFFLMVEGGQIDWAGHSNDAGTMLNEMVKFEEAVQGVYDWAKGREDTVILVTADHETGAFGLSYSSADLPEPQSKSGPAFAERDYAPNFNFGDFALLDSLYHQKASFSTLLSEFGALEEEQRTPARLMEMVNANSDFQIDEEQAEAVLADKPNPYHVEGHSYLEAEEVPAIQDFDAFYPYNDRGNVLGRVLGTAQNVVWGTGTHTHTPVNVFAWGPAETILPVSSIQHHSEVGQYLKSLVE 498
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491
   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  (0, 0)

(no "SCOP Domain" information available for 3WBH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WBH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WBH)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (B5BP20_9GAMM | B5BP20)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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