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(-) Description

Title :  ISOMERASE DOMAIN OF HUMAN GLUCOSE:FRUCTOSE-6-PHOSPHATE AMIDOTRANSFERASE
 
Authors :  Y. Nakaishi, M. Bando, K. Kondo, H. Tsuge
Date :  29 Feb 08  (Deposition) - 13 Jan 09  (Release) - 13 Jan 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Glucosamine-6-Phosphate Synthase, Aldose/Ketose Isomerase, Crystal Structure, Rossmann-Like Fold, Transferase, Alternative Splicing, Aminotransferase, Glutamine Amidotransferase, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Nakaishi, M. Bando, H. Shimizu, K. Watanabe, F. Goto, H. Tsuge, K. Kondo, M. Komatsu
Structural Analysis Of Human Glutamine:Fructose-6-Phosphate Amidotransferase, A Key Regulator In Type 2 Diabetes
Febs Lett. V. 583 163 2009
PubMed-ID: 19059404  |  Reference-DOI: 10.1016/J.FEBSLET.2008.11.041
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSAMINE--FRUCTOSE-6-PHOSPHATE AMINOTRANSFERASE [ISOMERIZING] 1
    ChainsA
    EC Number2.6.1.16
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET23
    Expression System StrainBL21(DE3)CODON+RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSIS(SUGAR ISOMERASE) DOMAINS, UNP RESIDUES 332- 699
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1AGP1Ligand/Ion2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1AGP2Ligand/Ion2-DEOXY-2-AMINO GLUCITOL-6-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:374 , THR A:375 , SER A:376 , SER A:420 , GLN A:421 , SER A:422 , THR A:425 , VAL A:471 , ALA A:472 , SER A:473 , LYS A:557 , GLU A:560 , HIS A:576 , HOH A:685 , HOH A:692 , HOH A:696 , HOH A:700 , HOH A:702 , HOH A:728BINDING SITE FOR RESIDUE AGP A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZJ4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZJ4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Asymmetric Unit (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_065345D366YGFPT1_HUMANDisease (CMS12)  ---AD347Y
2UniProtVAR_065346R403HGFPT1_HUMANDisease (CMS12)  ---AR384H
3UniProtVAR_065347R452HGFPT1_HUMANDisease (CMS12)  ---AR433H
4UniProtVAR_065348M509TGFPT1_HUMANDisease (CMS12)  ---AM490T
5UniProtVAR_065349M510TGFPT1_HUMANDisease (CMS12)  ---AM491T
6UniProtVAR_065350R514WGFPT1_HUMANDisease (CMS12)  ---AR495W
7UniProtVAR_065351R530WGFPT1_HUMANDisease (CMS12)  ---AR511W

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (7, 14)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_065345D366YGFPT1_HUMANDisease (CMS12)  ---AD347Y
2UniProtVAR_065346R403HGFPT1_HUMANDisease (CMS12)  ---AR384H
3UniProtVAR_065347R452HGFPT1_HUMANDisease (CMS12)  ---AR433H
4UniProtVAR_065348M509TGFPT1_HUMANDisease (CMS12)  ---AM490T
5UniProtVAR_065349M510TGFPT1_HUMANDisease (CMS12)  ---AM491T
6UniProtVAR_065350R514WGFPT1_HUMANDisease (CMS12)  ---AR495W
7UniProtVAR_065351R530WGFPT1_HUMANDisease (CMS12)  ---AR511W

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.GFPT1_HUMAN377-516
548-689
  2A:358-497
A:529-670
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SISPS51464 SIS domain profile.GFPT1_HUMAN377-516
548-689
  4A:358-497
A:529-670

(-) Exons   (0, 0)

(no "Exon" information available for 2ZJ4)

(-) 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:365
 aligned with GFPT1_HUMAN | Q06210 from UniProtKB/Swiss-Prot  Length:699

    Alignment length:365
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694     
          GFPT1_HUMAN   335 MKGNFSSFMQKEIFEQPESVVNTMRGRVNFDDYTVNLGGLKDHIKEIQRCRRLILIACGTSYHAGVATRQVLEELTELPVMVELASDFLDRNTPVFRDDVCFFLSQSGETADTLMGLRYCKERGALTVGITNTVGSSISRETDCGVHINAGPEIGVASTKAYTSQFVSLVMFALMMCDDRISMQERRKEIMLGLKRLPDLIKEVLSMDDEIQKLATELYHQKSVLIMGRGYHYATCLEGALKIKEITYMHSEGILAGELKHGPLALVDKLMPVIMIIMRDHTYAKCQNALQQVVARQGRPVVICDKEDTETIKNTKRTIKVPHSVDCLQGILSVIPLQLLAFHLAVLRGYDVDFPRNLAKSVTVE 699
               SCOP domains d2zj4a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SIS-2zj4A01 A:532-663                                                                                                               ----------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SIS-2zj4A02 A:532-663                                                                                                               ----------------- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhh..ee....ee.hhhhh.hhhhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhh.......eeeeeee....hhhhhhhhhhhhhh..eeeeee....hhhhhhh.eeee...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh....eeeee..hhhhhhhh..eeee......hhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------Y------------------------------------H------------------------------------------------H--------------------------------------------------------TT---W---------------W------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------SIS  PDB: A:358-497 UniProt: 377-516                                                                                                        -------------------------------SIS  PDB: A:529-670 UniProt: 548-689                                                                                                          ---------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zj4 A 316 MKGNFSSFMQKEIFEQPESVVNTMRGRVNFDDYTVNLGGLKDHIKEIQRCRRLILIACGTSYHAGVATRQVLEELTELPVMVELASDFLDRNTPVFRDDVCFFLSQSGETADTLMGLRYCKERGALTVGITNTVGSSISRETDCGVHINAGPEIGVASTKAYTSQFVSLVMFALMMCDDRISMQERRKEIMLGLKRLPDLIKEVLSMDDEIQKLATELYHQKSVLIMGRGYHYATCLEGALKIKEITYMHSEGILAGELKHGPLALVDKLMPVIMIIMRDHTYAKCQNALQQVVARQGRPVVICDKEDTETIKNTKRTIKVPHSVDCLQGILSVIPLQLLAFHLAVLRGYDVDFPRNLAKSVTVE 680
                                   325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675     

   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  (0, 0)

(no "CATH Domain" information available for 2ZJ4)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: SIS (53)
(-)
Family: SIS (23)
1aSIS-2zj4A01A:532-663
1bSIS-2zj4A02A:532-663

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A   (GFPT1_HUMAN | Q06210)
molecular function
    GO:0016597    amino acid binding    Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0004360    glutamine-fructose-6-phosphate transaminase (isomerizing) activity    Catalysis of the reaction: beta-D-fructose 6-phosphate + L-glutamine = D-glucosamine 6-phosphate + L-glutamate.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0036498    IRE1-mediated unfolded protein response    A series of molecular signals mediated by the endoplasmic reticulum stress sensor IRE1 (Inositol-requiring transmembrane kinase/endonuclease). Begins with activation of IRE1 in response to endoplasmic reticulum (ER) stress, and ends with regulation of a downstream cellular process, e.g. transcription. One target of activated IRE1 is the transcription factor HAC1 in yeast, or XBP1 in mammals; IRE1 cleaves an intron of a mRNA coding for HAC1/XBP1 to generate an activated HAC1/XBP1 transcription factor, which controls the up regulation of UPR-related genes. At least in mammals, IRE1 can also signal through additional intracellular pathways including JNK and NF-kappaB.
    GO:0006048    UDP-N-acetylglucosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    GO:0006047    UDP-N-acetylglucosamine metabolic process    The chemical reactions and pathways involving UDP-N-acetylglucosamine, a substance composed of N-acetylglucosamine, a common structural unit of oligosaccharides, in glycosidic linkage with uridine diphosphate.
    GO:1901137    carbohydrate derivative biosynthetic process    The chemical reactions and pathways resulting in the formation of carbohydrate derivative.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0032869    cellular response to insulin 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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0006112    energy reserve metabolic process    The chemical reactions and pathways by which a cell derives energy from stored compounds such as fats or glycogen.
    GO:0006002    fructose 6-phosphate metabolic process    The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
    GO:0006042    glucosamine biosynthetic process    The chemical reactions and pathways resulting in the formation of glucosamine (2-amino-2-deoxyglucopyranose), an aminodeoxysugar that occurs in combined form in chitin.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0045719    negative regulation of glycogen biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of glycogen.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0032868    response to insulin    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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0009744    response to sucrose    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 sucrose stimulus.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GFPT1_HUMAN | Q062102v4m 2zj3

(-) Related Entries Specified in the PDB File

2zj3 THE SAME PROTEIN COMPLEXED WITH ALPHA-D-GLUCOSE-6-PHOSPHATE