Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE A TP53-INDUCED GLYCOLYSIS AND APOPTOSIS REGULATOR PROTEIN FROM HOMO SAPIENS.
 
Authors :  J. G. Mccoy, C. A. Bingman, G. E. Wesenberg, G. N. Phillips Jr. , Center For Eukaryotic Structural Genomics (Cesg)
Date :  04 Jun 08  (Deposition) - 15 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Omim 610775, C12Orf5, Tigar, Tp53-Induced Glycolysis And Apoptosis Regulator, Casp Target, Structural Genomics Medical Relevance, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Isomerase, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. G. Mccoy, C. A. Bingman, G. E. Wesenberg, G. N. Phillips Jr.
Crystal Structure A Tp53-Induced Glycolysis And Apoptosis Regulator Protein From Homo Sapiens.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATOR PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPVP 16
    Expression System StrainB834 P(RARE2)
    Expression System Vector TypePLASMID
    GeneC12ORF5
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1MSE9Mod. Amino AcidSELENOMETHIONINE
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:10 , HIS A:11 , ASN A:17 , GLN A:23 , ARG A:61 , GLU A:89 , HIS A:198 , GLY A:199BINDING SITE FOR RESIDUE PO4 A 271

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DCY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Cys A:114 -Pro A:115

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DCY)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.TIGAR_HUMAN8-17  1A:8-17

(-) Exons   (0, 0)

(no "Exon" information available for 3DCY)

(-) 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:247
 aligned with TIGAR_HUMAN | Q9NQ88 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:269
                                 1                                                                                                                                                                                                                                                                       
                                 |   5        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         
          TIGAR_HUMAN     - -----MARFALTVVRHGETRFNKEKIIQGQGVDEPLSETGFKQAAAAGIFLNNVKFTHAFSSDLMRTKQTMHGILERSKFCKDMTVKYDSRLRERKYGVVEGKALSELRAMAKAAREECPVFTPPGGETLDQVKMRGIDFFEFLCQLILKEADQKEQFSQGSPSNCLETSLAEIFPLGKNHSSKVNSDSGIPGLAASVLVVSHGAYMRSLFDYFLTDLKCSLPATLSRSELMSVTPNTGMSLFIINFEEGREVKPTVQCICMNLQDHLN 264
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeeeeeeee...hhhhhhh...........hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhh.........eee.hhhh...hhhhh..hhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh---------hhhhhhhhh....-------------......eeeeeehhhhhhhhhhhhhhh.........hhhhhhh......eeeeeeee..ee....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PG_MUTASE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dcy A  -4 NLYFQSARFALTVVRHGETRFNKEKIIQGQGVDEPLSETGFKQAAAAGIFLNNVKFTHAFSSDLmRTKQTmHGILERSKFCKDmTVKYDSRLRERKYGVVEGKALSELRAmAKAAREECPVFTPPGGETLDQVKmRGIDFFEFLCQLILKEADQK---------NCLETSLAEIFPL-------------IPGLAASVLVVSHGAYmRSLFDYFLTDLKCSLPATLSRSELmSVTPNTGmSLFIINFEEGREVKPTVQCICmNLQDHLN 264
                                     5        15        25        35        45        55    |   65|       75   |    85        95       105|      115       125    |  135       145    |    -    |  165      |  -         -|      195      |205       215       225 |     235       245       255 |       
                                                                                           60-MSE |           79-MSE                    106-MSE                 130-MSE             150       160         172           186             202-MSE                  227-MSE 235-MSE               257-MSE   
                                                                                                 66-MSE                                                                                                                                                                                                  

   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 3DCY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DCY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DCY)

(-) Gene Ontology  (35, 35)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TIGAR_HUMAN | Q9NQ88)
molecular function
    GO:0004083    bisphosphoglycerate 2-phosphatase activity    Catalysis of the reaction: 2,3-bisphospho-D-glycerate + H(2)O = 3-phospho-D-glycerate + phosphate.
    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:0004331    fructose-2,6-bisphosphate 2-phosphatase activity    Catalysis of the reaction: D-fructose 2,6-bisphosphate + H2O = D-fructose-6-phosphate + 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: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).
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071279    cellular response to cobalt ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cobalt ion stimulus.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0030388    fructose 1,6-bisphosphate metabolic process    The chemical reactions and pathways involving fructose 1,6-bisphosphate, also known as FBP. The D enantiomer is a metabolic intermediate in glycolysis and gluconeogenesis.
    GO:0006003    fructose 2,6-bisphosphate metabolic process    The chemical reactions and pathways involving fructose 2,6-bisphosphate. The D enantiomer is an important regulator of the glycolytic and gluconeogenic pathways. It inhibits fructose 1,6-bisphosphatase and activates phosphofructokinase.
    GO:0060576    intestinal epithelial cell development    The process whose specific outcome is the progression of a columnar/cuboidal epithelial cell of the intestine over time, from its formation to the mature structure.
    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:1904024    negative regulation of glucose catabolic process to lactate via pyruvate    Any process that stops, prevents or reduces the frequency, rate or extent of glucose catabolic process to lactate via pyruvate.
    GO:0045820    negative regulation of glycolytic process    Any process that stops, prevents, or reduces the frequency, rate or extent of glycolysis.
    GO:1901525    negative regulation of macromitophagy    Any process that stops, prevents or reduces the frequency, rate or extent of macromitophagy.
    GO:1901215    negative regulation of neuron death    Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
    GO:0043069    negative regulation of programmed cell death    Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes.
    GO:2000378    negative regulation of reactive oxygen species metabolic process    Any process that stops, prevents or reduces the frequency, rate or extent of reactive oxygen species metabolic process.
    GO:0045739    positive regulation of DNA repair    Any process that activates or increases the frequency, rate or extent of DNA repair.
    GO:0010666    positive regulation of cardiac muscle cell apoptotic process    Any process that increases the rate or extent of cardiac cell apoptotic process, a form of programmed cell death induced by external or internal signals that trigger the activity of proteolytic caspases whose actions dismantle a cardiac muscle cell and result in its death.
    GO:1903301    positive regulation of hexokinase activity    Any process that activates or increases the frequency, rate or extent of hexokinase activity.
    GO:0043456    regulation of pentose-phosphate shunt    Any process that modulates the frequency, rate or extent of the pentose-phosphate shunt, the process in which glucose is oxidized, coupled to NADPH synthesis.
    GO:1902153    regulation of response to DNA damage checkpoint signaling    Any process that modulates the frequency, rate or extent of response to DNA damage checkpoint signaling.
    GO:0010332    response to gamma radiation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a gamma radiation stimulus. Gamma radiation is a form of electromagnetic radiation (EMR) or light emission of a specific frequency produced from sub-atomic particle interaction, such as electron-positron annihilation and radioactive decay. Gamma rays are generally characterized as EMR having the highest frequency and energy, and also the shortest wavelength, within the electromagnetic radiation spectrum.
    GO:0002931    response to ischemia    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a inadequate blood supply.
    GO:0009410    response to xenobiotic stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a xenobiotic compound stimulus. Xenobiotic compounds are compounds foreign to living organisms.
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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:114 - Pro A:115   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dcy
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TIGAR_HUMAN | Q9NQ88
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TIGAR_HUMAN | Q9NQ88
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3DCY)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3DCY)