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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI ALKALINE PHOSPHATASE D101A/D153A IN COMPLEX WITH INORGANIC PHOSPHATE
 
Authors :  A. Peck, D. Herschlag
Date :  13 Mar 15  (Deposition) - 29 Apr 15  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Sunden, A. Peck, J. Salzman, S. Ressl, D. Herschlag
Extensive Site-Directed Mutagenesis Reveals Interconnected Functional Units In The Alkaline Phosphatase Active Site.
Elife V. 4 2015
PubMed-ID: 25902402  |  Reference-DOI: 10.7554/ELIFE.06181

(-) Compounds

Molecule 1 - ALKALINE PHOSPHATASE
    Chains: A, B
    EC Number: 3.1.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-P2X
    Expression System Strain: SM547(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHOA, B0383, JW0374
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Strain: K12
    Synonym: APASE

 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
1GOL4Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:51 , SER A:102 , ASP A:327 , ASP A:369 , HIS A:370 , PO4 A:503binding site for residue ZN A 501
02AC2SOFTWAREASP A:327 , HIS A:331 , HIS A:412 , PO4 A:503binding site for residue ZN A 502
03AC3SOFTWAREASP A:51 , SER A:102 , ASP A:327 , LYS A:328 , HIS A:331 , ASP A:369 , HIS A:370 , HIS A:412 , ZN A:501 , ZN A:502 , HOH A:655binding site for residue PO4 A 503
04AC4SOFTWARETYR A:440 , GOL A:506 , ARG B:23binding site for residue GOL A 504
05AC5SOFTWAREALA A:101 , ALA A:103 , ASN A:117 , GLY A:118 , ARG A:166 , HOH A:605 , HOH A:615 , HOH A:655 , HOH A:694binding site for residue GOL A 505
06AC6SOFTWARELYS A:443 , SER A:450 , GOL A:504binding site for residue GOL A 506
07AC7SOFTWAREASP B:327 , HIS B:331 , HIS B:412 , PO4 B:503binding site for residue ZN B 501
08AC8SOFTWAREASP B:51 , ASP B:327 , ASP B:369 , HIS B:370 , PO4 B:503binding site for residue ZN B 502
09AC9SOFTWAREASP B:51 , ALA B:101 , SER B:102 , ARG B:166 , ASP B:327 , LYS B:328 , HIS B:331 , ASP B:369 , HIS B:370 , HIS B:412 , ZN B:501 , ZN B:502binding site for residue PO4 B 503
10AD1SOFTWAREALA B:101 , ASN B:117 , GLY B:118 , ARG B:166binding site for residue GOL B 504

(-) 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 4YR1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YR1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YR1)

(-) Exons   (0, 0)

(no "Exon" information available for 4YR1)

(-) 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:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhh......eeeeeee...hhhhhhhhhhhhhh......hhhhh.eeeeee..ee......ee...hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh...........hhhhhhhhh...hhhhh...hhhhhhhhhh..eeeeehhhhhhh..........hhhhhhhhh..eee.hhhhhhhh........eeee.........ee....eehhhhhh.....ee.........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......eee........eeeeee.....eeeeee..............eeeeee..hhhhhheeeehhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yr1 A   9 NRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTASAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQAATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLKSA 451
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448   


Chain B from PDB  Type:PROTEIN  Length:443
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhh.......eeeeeee...hhhhhhhhhhhhhh............eeeeee..ee......ee...hhhhhhhhhhhh..................hhhhhhhhh..eeeeeeeee..hhhhhh...........hhhhhhhhh...hhhhh...hhhhhhhhhh..eeeee..hhhhh..........hhhhhhhhh..eee.hhhhhhhh........eeee.........ee....eehhhhhh.....ee.........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee......eee........eeeeee.....eeeeee..............eeeeee..hhhhhheeeehhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yr1 B   9 NRAAQGDITAPGGARRLTGDQTAALRDSLSDKPAKNIILLIGDGMGDSEITAARNYAEGAGGFFKGIDALPLTGQYTHYALNKKTGKPDYVTASAASATAWSTGVKTYNGALGVDIHEKDHPTILEMAKAAGLATGNVSTAELQAATPAALVAHVTSRKCYGPSATSEKCPGNALEKGGKGSITEQLLNARADVTLGGGAKTFAETATAGEWQGKTLREQAQARGYQLVSDAASLNSVTEANQQKPLLGLFADGNMPVRWLGPKATYHGNIDKPAVTCTPNPQRNDSVPTLAQMTDKAIELLSKNEKGFFLQVEGASIDKQDHAANPCGQIGETVDLDEAVQRALEFAKKEGNTLVIVTADHAHASQIVAPDTKAPGLTQALNTKDGAVMVMSYGNSEEDSQEHTGSQLRIAAYGPHAANVVGLTDQTDLFYTMKAALGLKSA 451
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4YR1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YR1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YR1)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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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 1khj 1khk 1khl 1khn 1ura 1urb 1y6v 1y7a 2anh 2g9y 2ga3 2mlx 2mly 2mlz 3bdf 3bdg 3bdh 3cmr 3dpc 3dyc 3tg0 4km4 5c66 5gad 5gaf 5gag 5gah 5jtl 5jtm 5jtn 5jto 5jtp

(-) Related Entries Specified in the PDB File

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