Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF TAB5 ALKALINE PHOSPHATASE MUTANT HIS 135 ASP WITH MG BOUND IN THE M3 SITE.
 
Authors :  D. Koutsioulis, A. Lyskowski, S. Maki, E. Guthrie, G. Feller, V. Bouriotis, P. Heikinheimo
Date :  15 Dec 08  (Deposition) - 24 Nov 09  (Release) - 23 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Psychrophiles, Cold Adaptation, Alkaline Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Koutsioulis, A. Lyskowski, S. Maki, E. Guthrie, G. Feller, V. Bouriotis, P. Heikinheimo
Coordination Sphere Of The Third Metal Site Is Essential To The Activity And Metal Selectivity Of Alkaline Phosphatases.
Protein Sci. V. 19 75 2010
PubMed-ID: 19916164  |  Reference-DOI: 10.1002/PRO.284

(-) Compounds

Molecule 1 - ALKALINE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: ANTARCTIC BACTERIUM TAB5
    Organism Taxid: 82349
    Other Details: PHOSPHOSERINE RESIDUE AT POSITION 84. M1, M2 OCCUPIED BY ZN, M3 BY MG.
    Synonym: TAB5 ALKALINE PHOSPHATASE MUTANT

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2SEP2Mod. Amino AcidPHOSPHOSERINE
3ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESEP A:84 , ASP A:259 , HIS A:263 , HIS A:337 , HOH A:2332BINDING SITE FOR RESIDUE ZN A1376
2AC2SOFTWAREASP A:43 , SEP A:84 , ASP A:301 , HIS A:302BINDING SITE FOR RESIDUE ZN A1377
3AC3SOFTWAREASP A:43 , THR A:137 , GLU A:254 , HOH A:2064 , HOH A:2122 , HOH A:2231BINDING SITE FOR RESIDUE MG A1378
4AC4SOFTWAREASN A:266 , SER A:268 , HOH A:2214 , HOH A:2239 , HOH A:2242 , HOH A:2244BINDING SITE FOR RESIDUE MG A1379
5AC5SOFTWARESEP B:84 , ASP B:259 , HIS B:263 , HIS B:337 , HOH B:2257BINDING SITE FOR RESIDUE ZN B1376
6AC6SOFTWAREASP B:43 , SEP B:84 , ASP B:301 , HIS B:302BINDING SITE FOR RESIDUE ZN B1377
7AC7SOFTWAREASP B:43 , THR B:137 , GLU B:254 , HOH B:2054 , HOH B:2093 , HOH B:2170BINDING SITE FOR RESIDUE MG B1378
8AC8SOFTWAREASN B:266 , SER B:268 , HOH B:2176 , HOH B:2178 , HOH B:2180 , HOH B:2182BINDING SITE FOR RESIDUE MG B1379

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W5V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W5V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W5V)

(-) Exons   (0, 0)

(no "Exon" information available for 2W5V)

(-) 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:346
 aligned with Q9KWY4_9BACT | Q9KWY4 from UniProtKB/TrEMBL  Length:375

    Alignment length:346
                                    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      
         Q9KWY4_9BACT    30 QLKTPKNVILLISDGAGLSQISSTFYFKEGTPNYTQFKNIGLIKTSSSREDVTDSASGATAFSCGIKTYNAAIGVADDSTAVKSIVEIAALNNIKTGVVATSSITHATPASFYAHALNRGLEEEIAMDMTESDLDFFAGGGLNYFTKRKDKKDVLAILKGNQFTINTTGLTDFSSIASNRKMGFLLADEAMPTMEKGRGNFLSAATDLAIQFLSKDNSAFFIMSEGSQIDWGGHANNASYLISEINDFDDAIGTALAFAKKDGNTLVIVTSDHETGGFTLAAKKNKREDGSEYSDYTEIGPTFSTGGHSATLIPVFAYGPGSEEFIGIYENNEIFHKILKVTKWNQ 375
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...hhhhhhhhhhhh...hhhhhh.eeeeee.........hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh.........hhhhhhhhhh.....eeeee.hhhhhh.....hhhhhhhhh.eeee.....hhhhh....eeeee..............hhhhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...ee......eeeee.....eeeeeeee........ee...eeeeee..hhhhhheeee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w5v A  30 QLKTPKNVILLISDGAGLSQISSTFYFKSGTPNYTQFKNIGLIKTSSSREDVTDsASGATAFSCGIKTYNAAIGVADDSTAVKSIVEIAALNNIKTGVVATSSITDATPASFYAHALNRGLEEEIAMDMTESDLDFFAGGGLNYFTKRKDKKDVLAILKGNQFTINTTALTDFSSIASNRKMGFLLADEAMPTMEKGRGNFLSAATDLAIQFLSKDNSAFFIMSEGSQIDWGGHANNASYLISEINDFDDAIGTALAFAKKDGNTLVIVTSDHETGGFTLAAKKNKREDGSEYSDYTEIGPTFSTGGHSATLIPVFAYGPGSEEFIGIYENNEIFHKILKVTKWNQ 375
                                    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      
                                                                                 84-SEP                                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:346
 aligned with Q9KWY4_9BACT | Q9KWY4 from UniProtKB/TrEMBL  Length:375

    Alignment length:346
                                    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      
         Q9KWY4_9BACT    30 QLKTPKNVILLISDGAGLSQISSTFYFKEGTPNYTQFKNIGLIKTSSSREDVTDSASGATAFSCGIKTYNAAIGVADDSTAVKSIVEIAALNNIKTGVVATSSITHATPASFYAHALNRGLEEEIAMDMTESDLDFFAGGGLNYFTKRKDKKDVLAILKGNQFTINTTGLTDFSSIASNRKMGFLLADEAMPTMEKGRGNFLSAATDLAIQFLSKDNSAFFIMSEGSQIDWGGHANNASYLISEINDFDDAIGTALAFAKKDGNTLVIVTSDHETGGFTLAAKKNKREDGSEYSDYTEIGPTFSTGGHSATLIPVFAYGPGSEEFIGIYENNEIFHKILKVTKWNQ 375
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...hhhhhhhh.......hhhhhh.eeeeee.........hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh.........hhhhhhhhhh.....eeeee.hhhhhh.....hhhhhhhh..eeee.....hhhhhh...eeeee.......hhhhh..hhhhhhhhhhhhhhhhhhh.eeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee...ee......eeeee.....eeeeeeee........ee...eeeeee..hhhhhheeee.hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w5v B  30 QLKTPKNVILLISDGAGLSQISSTFYFKSGTPNYTQFKNIGLIKTSSSREDVTDsASGATAFSCGIKTYNAAIGVADDSTAVKSIVEIAALNNIKTGVVATSSITDATPASFYAHALNRGLEEEIAMDMTESDLDFFAGGGLNYFTKRKDKKDVLAILKGNQFTINTTALTDFSSIASNRKMGFLLADEAMPTMEKGRGNFLSAATDLAIQFLSKDNSAFFIMSEGSQIDWGGHANNASYLISEINDFDDAIGTALAFAKKDGNTLVIVTSDHETGGFTLAAKKNKREDGSEYSDYTEIGPTFSTGGHSATLIPVFAYGPGSEEFIGIYENNEIFHKILKVTKWNQ 375
                                    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      
                                                                                 84-SEP
   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 2W5V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W5V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W5V)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q9KWY4_9BACT | Q9KWY4)
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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2w5v)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2w5v
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9KWY4_9BACT | Q9KWY4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9KWY4_9BACT | Q9KWY4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9KWY4_9BACT | Q9KWY4: 2iuc 2w5w 2w5x

(-) Related Entries Specified in the PDB File

2iuc STRUCTURE OF ALKALINE PHOSPHATASE FROM THE ANTARCTIC BACTERIUM TAB5
2w5w STRUCTURE OF TAB5 ALKALINE PHOSPHATASE MUTANT
2w5x STRUCTURE OF TAB5 ALKALINE PHOSPHATASE MUTANT HIS 135 GLU WITH MG BOUND IN THE M3 SITE.