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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN IPP ISOMERASE I IN SPACE GROUP P212121
 
Authors :  C. Zhang, Z. Wei, W. Gong
Date :  24 Mar 06  (Deposition) - 05 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Protein, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Zhang, L. Liu, H. Xu, Z. Wei, Y. Wang, Y. Lin, W. Gong
Crystal Structures Of Human Ipp Isomerase: New Insights Into The Catalytic Mechanism
J. Mol. Biol. V. 366 1437 2007
PubMed-ID: 17137593  |  Reference-DOI: 10.1016/J.JMB.2006.10.092
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE 1
    ChainsA
    EC Number5.3.3.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIPP ISOMERASE 1, ISOPENTENYL PYROPHOSPHATE ISOMERASE 1, IPPI1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
1CL10Ligand/IonCHLORIDE ION
2MN8Ligand/IonMANGANESE (II) ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:40 , HIS A:51 , HIS A:88 , GLU A:146 , GLU A:148BINDING SITE FOR RESIDUE MN A 1001
02AC2SOFTWAREHIS A:135 , HIS A:147 , HOH A:3030 , HOH A:3050 , HOH A:3053 , HOH A:3067BINDING SITE FOR RESIDUE MN A 1002
03AC3SOFTWARELYS A:137 , HOH A:3012 , HOH A:3013 , HOH A:3016 , HOH A:3024 , HOH A:3025BINDING SITE FOR RESIDUE MN A 1003
04AC4SOFTWARETYR A:136 , GLU A:148 , ASP A:150 , HOH A:3047 , HOH A:3190BINDING SITE FOR RESIDUE MN A 1004
05AC5SOFTWAREHOH A:3116 , HOH A:3148 , HOH A:3167 , HOH A:3211 , HOH A:3247 , HOH A:3271BINDING SITE FOR RESIDUE MN A 1005
06AC6SOFTWARECYS A:85 , ARG A:111 , GLU A:115BINDING SITE FOR RESIDUE MN A 1006
07AC7SOFTWARECYS A:80 , ILE A:193 , HOH A:3296BINDING SITE FOR RESIDUE MN A 1007
08AC8SOFTWAREGLU A:97 , SER A:99 , HOH A:3301 , HOH A:3302 , HOH A:3303BINDING SITE FOR RESIDUE MN A 1008
09AC9SOFTWARETYR A:171 , CL A:3001 , HOH A:3011 , HOH A:3013BINDING SITE FOR RESIDUE NA A 2001
10BC1SOFTWAREASP A:210 , ASN A:211 , LEU A:212 , ASN A:213 , HIS A:214 , HOH A:3045 , HOH A:3109 , HOH A:3289BINDING SITE FOR RESIDUE NA A 2002
11BC2SOFTWARELYS A:137 , SER A:170 , TYR A:171 , NA A:2001 , HOH A:3143BINDING SITE FOR RESIDUE CL A 3001
12BC3SOFTWARELYS A:113 , PRO A:119 , LEU A:120 , HOH A:3080BINDING SITE FOR RESIDUE CL A 3002
13BC4SOFTWAREASN A:63 , LYS A:176 , HOH A:3117BINDING SITE FOR RESIDUE CL A 3003
14BC5SOFTWAREASN A:63 , ASN A:92 , ARG A:156 , ASN A:213 , HOH A:3082 , HOH A:3109BINDING SITE FOR RESIDUE CL A 3004
15BC6SOFTWAREGLN A:15 , HIS A:214 , ASN A:216 , GLN A:217 , HOH A:3308BINDING SITE FOR RESIDUE CL A 3005
16BC7SOFTWAREPHE A:77 , PRO A:195 , TRP A:196 , HOH A:3163BINDING SITE FOR RESIDUE CL A 3006
17BC8SOFTWAREASN A:44BINDING SITE FOR RESIDUE CL A 3007
18BC9SOFTWAREHOH A:3316BINDING SITE FOR RESIDUE CL A 3008
19CC1SOFTWARELYS A:198 , HOH A:3155 , HOH A:3200BINDING SITE FOR RESIDUE CL A 3009

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:21 -A:39

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.IDI1_HUMAN49-199  1A:49-199

(-) Exons   (0, 0)

(no "Exon" information available for 2DHO)

(-) 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:215
 aligned with IDI1_HUMAN | Q13907 from UniProtKB/Swiss-Prot  Length:227

    Alignment length:215
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     
           IDI1_HUMAN    13 QVQLLAEMCILIDENDNKIGAETKKNCHLNENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRKNVTLNPDPNEIKSYCYVSKEELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM 227
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.....eeeeeehhhhhhhhhhh....eeeeeeeee.....eeeeee..........ee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeehhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh....hhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------NUDIX  PDB: A:49-199 UniProt: 49-199                                                                                                                   ---------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dho A  13 QVQLLAEMCILIDENDNKIGAETKKNCHLNENIEKGLLHRAFSVFLFNTENKLLLQQRSDAKITFPGCFTNTCCSHPLSNPAELEESDALGVRRAAQRRLKAELGIPLEEVPPEEINYLTRIHYKAQSDGIWGEHEIDYILLVRMNVTLNPDPNEIKSYCYVSKEELKELLKKAASGEIKITPWFKIIAATFLFKWWDNLNHLNQFVDHEKIYRM 227
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222     

   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 2DHO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IDI1_HUMAN | Q13907)
molecular function
    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:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0004452    isopentenyl-diphosphate delta-isomerase activity    Catalysis of the reaction: isopentenyl diphosphate = dimethylallyl diphosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006695    cholesterol biosynthetic process    The chemical reactions and pathways resulting in the formation of cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0008203    cholesterol metabolic process    The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
    GO:0050992    dimethylallyl diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of dimethylallyl diphosphate.
    GO:0008299    isoprenoid biosynthetic process    The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0006694    steroid biosynthetic process    The chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus; includes de novo formation and steroid interconversion by modification.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0016126    sterol biosynthetic process    The chemical reactions and pathways resulting in the formation of sterols, steroids with one or more hydroxyl groups and a hydrocarbon side-chain in the molecule.
cellular component
    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:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IDI1_HUMAN | Q139072i6k 2icj 2ick

(-) Related Entries Specified in the PDB File

2ewq CRYSTAL STRUCTURE OF HUMAN IPPI IN SPACE GROUP C2