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(-) Description

Title :  E. COLI ALKALINE PHOSPHATASE MUTANT (D153HD330N) MIMIC OF THE TRANSITION STATES WITH ALUMINIUM FLUORIDE
 
Authors :  M. H. Le Du, C. Lamoure, B. H. Muller, O. V. Bulgakov, E. Lajeunesse, A. M J. C. Boulain
Date :  30 Nov 01  (Deposition) - 13 Mar 02  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alkaline Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. H. Le Du, C. Lamoure, B. H. Muller, O. V. Bulgakov, E. Lajeunesse, A. Menez, J. C. Boulain
Artificial Evolution Of An Enzyme Active Site: Structural Studies Of Three Highly Active Mutants Of Escherichia Coli Alkaline Phosphatase.
J. Mol. Biol. V. 316 941 2002
PubMed-ID: 11884134  |  Reference-DOI: 10.1006/JMBI.2001.5384
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALKALINE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PLIP4.0D153HD330N
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: WCC118

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1AF32Ligand/IonALUMINUM FLUORIDE
2ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:327 , HIS A:331 , HIS A:412 , AF3 A:453 , HOH A:1003BINDING SITE FOR RESIDUE ZN A 450
2AC2SOFTWAREASP A:51 , SER A:102 , ASP A:369 , HIS A:370 , AF3 A:453BINDING SITE FOR RESIDUE ZN A 451
3AC3SOFTWAREASP B:327 , HIS B:331 , HIS B:412 , AF3 B:453BINDING SITE FOR RESIDUE ZN B 450
4AC4SOFTWAREASP B:51 , SER B:102 , ASP B:369 , HIS B:370 , AF3 B:453BINDING SITE FOR RESIDUE ZN B 451
5AC5SOFTWAREASP A:51 , ASP A:101 , SER A:102 , HIS A:153 , ARG A:166 , ASP A:327 , HIS A:370 , HIS A:412 , ZN A:450 , ZN A:451 , HOH A:1001 , HOH A:1002 , HOH A:1003BINDING SITE FOR RESIDUE AF3 A 453
6AC6SOFTWAREASP B:101 , SER B:102 , HIS B:153 , ARG B:166 , ASP B:327 , HIS B:370 , HIS B:412 , ZN B:450 , ZN B:451 , HOH B:1004 , HOH B:1006BINDING SITE FOR RESIDUE AF3 B 453

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:168 -A:178
2A:286 -A:336
3B:168 -B:178
4B:286 -B:336

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALKALINE_PHOSPHATASEPS00123 Alkaline phosphatase active site.PPB_ECOLI121-129
 		  2A:99-107
B:99-107

(-) Exons   (0, 0)

(no "Exon" information available for 1KHJ)

(-) 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:444
 aligned with PPB_ECOLI | P00634 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:444
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467    
            PPB_ECOLI    28 VLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 471
               SCOP domains d1khja_ A: Alkaline phosphatase                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1khjA00 A:6-449 Alkaline Phosphatase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................hhhhhhhh.......eeeeeee...hhhhhhhhhhhhh.......hhhhh.eeeeee..ee......ee...hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhhhhh........hhhhhhhhh...........hhhhhhhhhh..eeeee.hhhhhh..........hhhhhhhhh..eee.hhhhhhh.........eeee.........ee....eehhhhhh.....ee.........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......eee........eeeeee.....eeeeee..............eeeeee..hhhhhheeeehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------ALKALINE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1khj A   6 VLENRAAQGNITAPGGARRLTGDQTAALRNSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQHATPAALVAHVTSRKCYGPSATSQKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREEAEARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQNHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 449
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445    


Chain B from PDB  Type:PROTEIN  Length:444
 aligned with PPB_ECOLI | P00634 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:444
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467    
            PPB_ECOLI    28 VLENRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQDATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 471
               SCOP domains d1khjb_ B: Alkaline phosphatase                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1khjB00 B:6-449 Alkaline Phosphatase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alk_phosphatase-1khjB01 B:405-448           - Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alk_phosphatase-1khjB02 B:405-448           - Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alk_phosphatase-1khjB03 B:405-448           - Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Alk_phosphatase-1khjB04 B:405-448           - Pfam domains (4)
         Sec.struct. author .......................hhhhhhhh.......eeeeeee...hhhhhhhhhhhhhh......hhhhh.eeeeee..ee......ee...hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh...........hhhhhhhhh...hhhhh...hhhhhhhhhh..eeeeehhhhhhh..........hhhhhhhhh..eee.hhhhhhh.........eeee.........ee....eehhhhhh.....ee.........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......eee........eeeeee.....eeeeee..............eeeeee..hhhhhheeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------ALKALINE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1khj B   6 VLENRAAQGNITAPGGARRLTGDQTAALRNSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTDSAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQHATPAALVAHVTSRKCYGPSATSQKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREEAEARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQNHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLK 449
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Alk_phosphatase (47)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PPB_ECOLI | P00634)
molecular function
    GO:0004035    alkaline phosphatase activity    Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum.
    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:0033748    hydrogenase (acceptor) activity    Catalysis of the reaction: H2 + A = AH2.
    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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0030613    oxidoreductase activity, acting on phosphorus or arsenic in donors    Catalysis of an oxidation-reduction (redox) reaction in which a phosphorus- or arsenic-containing group acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1khj
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 Related Entries

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

UniProtKB/Swiss-Prot
        PPB_ECOLI | P00634: 1aja 1ajb 1ajc 1ajd 1alh 1ali 1alj 1alk 1ani 1anj 1b8j 1ed8 1ed9 1elx 1ely 1elz 1ew8 1ew9 1hjk 1hqa 1kh4 1kh5 1kh7 1kh9 1khk 1khl 1khn 1ura 1urb 1y6v 1y7a 2anh 2g9y 2ga3 2mlx 2mly 2mlz 3bdf 3bdg 3bdh 3cmr 3dpc 3dyc 3tg0 4km4 4yr1 5c66 5gad 5gaf 5gag 5gah 5jtl 5jtm 5jtn 5jto 5jtp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1KHJ)