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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ENOLASE-PHOSPHATASE E1
 
Authors :  H. Wang, H. Pang, M. Bartlam, Z. Rao
Date :  23 May 05  (Deposition) - 21 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Structure Human Enolase-Phosphatase E1, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Wang, H. Pang, M. Bartlam, Z. Rao
Crystal Structure Of Human E1 Enzyme And Its Complex With A Substrate Analog Reveals The Mechanism Of Its Phosphatase/Enolase
J. Mol. Biol. V. 348 917 2005
PubMed-ID: 15843022  |  Reference-DOI: 10.1016/J.JMB.2005.01.072
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - E-1 ENZYME
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymENOLASE-PHOSPHATASE E1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:16 , GLU A:18 , ASP A:212 , HOH A:1260 , HOH A:1261 , HOH A:1262BINDING SITE FOR RESIDUE MG A 1257
2AC2SOFTWAREASP A:198 , HOH A:1263 , HOH A:1264 , HOH A:1265 , HOH A:1266 , HOH A:1267BINDING SITE FOR RESIDUE MG A 1258
3AC3SOFTWAREHOH A:1268 , HOH A:1269 , HOH A:1270 , HOH A:1271 , HOH A:1272 , HOH A:1273BINDING SITE FOR RESIDUE MG A 1259

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ZS9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZS9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZS9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZS9)

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002739201aENSE00001296627chr4:83351715-83352066352ENOPH_HUMAN1-28281A:4-2825
1.2ENST000002739202ENSE00001152365chr4:83369073-83369174102ENOPH_HUMAN29-62341A:29-6234
1.3ENST000002739203ENSE00001073195chr4:83372196-83372398203ENOPH_HUMAN63-130681A:63-130 (gaps)68
1.4ENST000002739204ENSE00000969818chr4:83375875-83376007133ENOPH_HUMAN130-174451A:130-17445
1.5ENST000002739205ENSE00001385975chr4:83378068-83378191124ENOPH_HUMAN175-216421A:175-21642
1.6cENST000002739206cENSE00001150347chr4:83381134-833822441111ENOPH_HUMAN216-261461A:216-25742

(-) 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:253
 aligned with ENOPH_HUMAN | Q9UHY7 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:254
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253    
          ENOPH_HUMAN     4 LSVPAEVTVILLDIEGTTTPIAFVKDILFPYIEENVKEYLQTHWEEEECQQDVSLLRKQAEEDAHLDGAVPIPAASGNGVDDLQQMIQAVVDNVCWQMSLDRKTTALKQLQGHMWRAAFTAGRMKAEFFADVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHSTEGDILELVDGHFDTKIGHKVESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAGLTDDEKTYYSLITSFSELYL 257
               SCOP domains d1zs9a1 A:4-256 E-1 enzyme                                                                                                                                                                                                                                   - SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------HAD_2-1zs9A01 A:13-230                                                                                                                                                                                                    --------------------------- Pfam domains
         Sec.struct. author ........eeee.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh.-.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh..eeeee...hhhhhhhhhhh.....hhhhh.eeehhhhh...hhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh..eeeee........hhhhhhhh.ee.hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:4-28   Exon 1.2  PDB: A:29-62            Exon 1.3  PDB: A:63-130 (gaps) UniProt: 63-130                      --------------------------------------------Exon 1.5  PDB: A:175-216 UniProt: 175-216 ----------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:130-174 UniProt: 130-174    -----------------------------------------Exon 1.6c  PDB: A:216-257 UniProt: 216-261 Transcript 1 (2)
                 1zs9 A   4 LSVPAEVTVILLDIEGTTTPIAFVKDILFPYIEENVKEYLQTHWEEEECQQDVSLLRKQAEEDAHLDGAVPIPAASGNGVDDLQQmIQAVVDNVCWQmSLD-KTTALKQLQGHmWRAAFTAGRmKAEFFADVVPAVRKWREAGmKVYIYSSGSVEAQKLLFGHSTEGDILELVDGHFDTKIGHKVESESYRKIADSIGCSTNNILFLTDVTREASAAEEADVHVAVVVRPGNAGLTDDEKTYYSLITSFSELYL 257
                                    13        23        33        43        53        63        73        83     |  93       103| |    113   |   123   |   133       143   |   153       163       173       183       193       203       213       223       233       243       253    
                                                                                                                89-MSE     101-MSE|        117-MSE   127-MSE             147-MSE                                                                                                          
                                                                                                                              104 |                                                                                                                                                       
                                                                                                                                106                                                                                                                                                       

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  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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1ZS9)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: HAD (186)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ENOPH_HUMAN | Q9UHY7)
molecular function
    GO:0043874    acireductone synthase activity    Catalysis of the reactions: 5-(methylthio)-2,3-dioxopentyl phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate; (1a) 5-(methylthio)-2,3-dioxopentyl phosphate = 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate; (1b) 2-hydroxy-5-(methylthio)-3-oxopent-1-enyl phosphate + H2O = 1,2-dihydroxy-5-(methylthio)pent-1-en-3-one + phosphate.
    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.
biological process
    GO:0019509    L-methionine salvage from methylthioadenosine    The generation of L-methionine (2-amino-4-(methylthio)butanoic acid) from methylthioadenosine.
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    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:0009086    methionine biosynthetic process    The chemical reactions and pathways resulting in the formation of methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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        ENOPH_HUMAN | Q9UHY71yns

(-) Related Entries Specified in the PDB File

1yns STRUCTURE OF HUMAN E1 ENZYME AND ITS COMPLEX WITH A SUBSTRATE ANALOG