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(-) Description

Title :  ALKALINE PHOSPHATASE FROM HUMAN PLACENTA IN COMPLEX WITH P-NITROPHENYL-PHOSPHONATE
 
Authors :  P. Llinas, E. A. Stura, A. Menez, Z. Kiss, T. Stigbrand, J. L. Millan, M. H
Date :  18 Apr 05  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alkaline Phosphatase, Phosphoserine, Substrate Analog, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Llinas, E. A. Stura, A. Menez, Z. Kiss, T. Stigbrand, J. L. Millan, M. H. Le Du
Structural Studies Of Human Placental Alkaline Phosphatase In Complex With Functional Ligands.
J. Mol. Biol. V. 350 441 2005
PubMed-ID: 15946677  |  Reference-DOI: 10.1016/J.JMB.2005.04.068

(-) Compounds

Molecule 1 - ALKALINE PHOSPHATASE
    ChainsA
    EC Number3.1.3.1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPLAP-1, REGAN ISOZYME
    TissuePLACENTA

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric Unit (6, 9)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MG1Ligand/IonMAGNESIUM ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PNP2Ligand/IonMETHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER
5PO31Ligand/IonPHOSPHITE ION
6ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MG-1Ligand/IonMAGNESIUM ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PNP4Ligand/IonMETHYL-PHOSPHONIC ACID MONO-(4-NITRO-PHENYL) ESTER
5PO32Ligand/IonPHOSPHITE ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:122 , LEU A:258 , ARG A:297 , HOH A:1019 , HOH A:1331 , HOH A:1358 , HOH A:1360 , HOH A:1441 , HOH A:1516 , HOH A:1525 , HOH A:1536 , HOH A:1546 , HOH A:1593 , HOH A:1594BINDING SITE FOR RESIDUE NAG A 801
2AC2SOFTWARETRP A:248 , ASN A:249 , GLU A:252 , HOH A:988 , HOH A:1214 , HOH A:1341 , HOH A:1379 , HOH A:1418 , HOH A:1599BINDING SITE FOR RESIDUE NAG A 803
3AC3SOFTWAREASP A:316 , HIS A:320 , HIS A:432 , PO3 A:907 , HOH A:1661BINDING SITE FOR RESIDUE ZN A 903
4AC4SOFTWAREASP A:42 , SER A:92 , ASP A:357 , HIS A:358 , PO3 A:907BINDING SITE FOR RESIDUE ZN A 904
5AC5SOFTWAREASP A:42 , SER A:155 , GLU A:311 , HOH A:949 , HOH A:969 , HOH A:1038BINDING SITE FOR RESIDUE MG A 905
6AC6SOFTWAREGLU A:216 , PHE A:269 , GLU A:270 , ASP A:285 , HOH A:1081BINDING SITE FOR RESIDUE CA A 906
7AC7SOFTWAREASP A:42 , SER A:92 , HIS A:153 , ARG A:166 , ASP A:316 , HIS A:358 , HIS A:432 , PNP A:901 , ZN A:903 , ZN A:904 , HOH A:969 , HOH A:1661 , HOH A:1667BINDING SITE FOR RESIDUE PO3 A 907
8AC8SOFTWAREASP A:91 , PHE A:107 , GLN A:108 , ARG A:166 , TYR A:367 , HIS A:432 , PO3 A:907 , HOH A:1625 , HOH A:1662BINDING SITE FOR RESIDUE PNP A 901
9AC9SOFTWAREARG A:125 , GLY A:126 , ARG A:250 , LEU A:253 , MET A:254 , SER A:257 , GLU A:290 , GLU A:293 , ALA A:294 , ARG A:297 , HOH A:1664 , HOH A:1665 , HOH A:1666BINDING SITE FOR RESIDUE PNP A 902

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:121 -A:183
2A:467 -A:474

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017419P25LPPB1_HUMANPolymorphism1130335AP3L
2UniProtVAR_050520I89LPPB1_HUMANPolymorphism13026692AI67L
3UniProtVAR_050521R231PPPB1_HUMANPolymorphism1048988AR209P
4UniProtVAR_050522R263HPPB1_HUMANPolymorphism2853378AR241H
5UniProtVAR_050523E451GPPB1_HUMANPolymorphism1048994AE429G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 10)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_017419P25LPPB1_HUMANPolymorphism1130335AP3L
2UniProtVAR_050520I89LPPB1_HUMANPolymorphism13026692AI67L
3UniProtVAR_050521R231PPPB1_HUMANPolymorphism1048988AR209P
4UniProtVAR_050522R263HPPB1_HUMANPolymorphism2853378AR241H
5UniProtVAR_050523E451GPPB1_HUMANPolymorphism1048994AE429G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALKALINE_PHOSPHATASEPS00123 Alkaline phosphatase active site.PPB1_HUMAN111-119  1A:89-97
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALKALINE_PHOSPHATASEPS00123 Alkaline phosphatase active site.PPB1_HUMAN111-119  2A:89-97

(-) Exons   (11, 11)

Asymmetric Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003920271aENSE00001510465chr2:233243244-233243588345PPB1_HUMAN1-26261A:1-44
1.2ENST000003920272ENSE00001789454chr2:233243681-233243797117PPB1_HUMAN26-65401A:4-4340
1.3ENST000003920273ENSE00001730171chr2:233243910-233244025116PPB1_HUMAN65-103391A:43-8139
1.4aENST000003920274aENSE00001645266chr2:233244223-233244397175PPB1_HUMAN104-162591A:82-14059
1.4cENST000003920274cENSE00001620414chr2:233244474-233244646173PPB1_HUMAN162-219581A:140-19758
1.5ENST000003920275ENSE00001765153chr2:233244896-233245030135PPB1_HUMAN220-264451A:198-24245
1.6ENST000003920276ENSE00001641289chr2:233245130-23324520273PPB1_HUMAN265-289251A:243-26725
1.7ENST000003920277ENSE00001723793chr2:233245333-233245467135PPB1_HUMAN289-334461A:267-31246
1.8ENST000003920278ENSE00001789464chr2:233245550-233245741192PPB1_HUMAN334-398651A:312-37665
1.9bENST000003920279bENSE00001737846chr2:233245961-233246077117PPB1_HUMAN398-437401A:376-41540
1.10bENST0000039202710bENSE00001510464chr2:233246207-2332475991393PPB1_HUMAN437-535991A:415-48167

(-) Sequences/Alignments

Asymmetric 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:481
 aligned with PPB1_HUMAN | P05187 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:481
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502 
           PPB1_HUMAN    23 IIPVEEENPDFWNREAAEALGAAKKLQPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKKDKLGPEIPLAMDRFPYVALSKTYNVDKHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTRGNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVPASARQEGCQDIATQLISNMDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAKRQGARYVWNRTELMQASLDPSVTHLMGLFEPGDMKYEIHRDSTLDPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSHVFSFGGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPPAG 503
               SCOP domains d1zeda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1zedA00 A:1-481 Alkaline Phosphatase, subunit A                                                                                                                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------Alk_phosphatase-1zedA01 A:33-468                                                                                                                                                                                                                                                                                                                                                                                                                    ------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...hhhhhhhhhhhhhhhh.........hhhhh.eeeeee.........hhhhhhhhhhhh.................hhhhh......hhhhhhhhh..eeeeeeeee..hhhhhh...........hhhhhhhhhhhh...hhhhhhhhh....eeeeehhhhhh...........hhhhh.......hhhhhhhhh...eeee.hhhhhhhhhh.....eeeee.......hhhhh......hhhhhhhhhhhhhh.....eeeeeee.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..ee.eee..........................eeeee..............hhhhhh.......eee......ee...eeeeee..hhhhh..eee.hhhhhhhhhhh.hhhhh......... Sec.struct. author
                 SAPs(SNPs) --L---------------------------------------------------------------L---------------------------------------------------------------------------------------------------------------------------------------------P-------------------------------H-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------G---------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------ALKALINE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) 1.1a--------------------------------------Exon 1.3  PDB: A:43-81 UniProt: 65-103 Exon 1.4a  PDB: A:82-140 UniProt: 104-162                  ---------------------------------------------------------Exon 1.5  PDB: A:198-242 UniProt: 220-264    Exon 1.6  PDB: A:243-267 --------------------------------------------Exon 1.8  PDB: A:312-376 UniProt: 334-398                        --------------------------------------Exon 1.10b  PDB: A:415-481 UniProt: 437-535 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2  PDB: A:4-43 UniProt: 26-65    ------------------------------------------------------------------------------------------------Exon 1.4c  PDB: A:140-197 UniProt: 162-219                ---------------------------------------------------------------------Exon 1.7  PDB: A:267-312 UniProt: 289-334     ---------------------------------------------------------------Exon 1.9b  PDB: A:376-415               ------------------------------------------------------------------ Transcript 1 (2)
                 1zed A   1 IIPVEEENPDFWNREAAEALGAAKKLQPAQTAAKNLIIFLGDGMGVSTVTAARILKGQKKDKLGPEIPLAMDRFPYVALSKTYNVDKHVPDSGATATAYLCGVKGNFQTIGLSAAARFNQCNTTRGNEVISVMNRAKKAGKSVGVVTTTRVQHASPAGTYAHTVNRNWYSDADVPASARQEGCQDIATQLISNMDIDVILGGGRKYMFRMGTPDPEYPDDYSQGGTRLDGKNLVQEWLAKRQGARYVWNRTELMQASLDPSVTHLMGLFEPGDMKYEIHRDSTLDPSLMEMTEAALRLLSRNPRGFFLFVEGGRIDHGHHESRAYRALTETIMFDDAIERAGQLTSEEDTLSLVTADHSHVFSFGGYPLRGSSIFGLAPGKARDRKAYTVLLYGNGPGYVLKDGARPDVTESESGSPEYRQQSAVPLDEETHAGEDVAVFARGPQAHLVHGVQEQTFIAHVMAFAACLEPYTACDLAPPAG 481
                                    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       480 

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (PPB1_HUMAN | P05187)
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: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: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.
cellular component
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPB1_HUMAN | P051871ew2 1zeb 1zef 2glq 3mk0 3mk1 3mk2

(-) Related Entries Specified in the PDB File

1ew2 1zeb 1zef