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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE AMF
 
Authors :  N. Tanaka, A. Haga, N. Naba, K. Shiraiwa, Y. Kusakabe, K. Hashimoto, T. F H. Nagase, A. Raz, K. T. Nakamura
Date :  10 Jun 05  (Deposition) - 23 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Tanaka, A. Haga, N. Naba, K. Shiraiwa, Y. Kusakabe, K. Hashimoto, T. Funasaka, H. Nagase, A. Raz, K. T. Nakamura
Crystal Structures Of Mouse Autocrine Motility Factor In Complex With Carbohydrate Phosphate Inhibitors Provide Insight Into Structure-Activity Relationship Of The Inhibitors
J. Mol. Biol. V. 356 312 2006
PubMed-ID: 16375918  |  Reference-DOI: 10.1016/J.JMB.2005.11.076

(-) Compounds

Molecule 1 - GLUCOSE-6-PHOSPHATE ISOMERASE
    ChainsA, B
    EC Number5.3.1.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymCYTOKINE, GPI, PHOSPHOGLUCOSE ISOMERASE, PGI, PHOSPHOHEXOSE ISOMERASE, PHI, NEUROLEUKIN, NLK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL4Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:160 , SER A:210 , LYS A:211 , THR A:215BINDING SITE FOR RESIDUE ACT A 801
2AC2SOFTWAREASP A:140 , TRP A:141 , LYS A:142 , LYS A:241 , HOH A:1091BINDING SITE FOR RESIDUE GOL A 701
3AC3SOFTWAREILE A:549 , ARG A:553 , HOH A:1050 , GLY B:419 , LYS B:423 , LEU B:426 , HOH B:1038BINDING SITE FOR RESIDUE GOL A 702
4AC4SOFTWAREARG B:135 , TRP B:141 , LYS B:142 , HOH B:857BINDING SITE FOR RESIDUE GOL B 703
5AC5SOFTWAREGLY A:419 , HIS A:422 , LYS A:423 , LEU A:426 , HOH A:935 , HOH A:1055 , ILE B:549 , ARG B:553BINDING SITE FOR RESIDUE GOL A 704

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:384 -Thr A:385
2Gly B:384 -Thr B:385

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1P_GLUCOSE_ISOMERASE_3PS51463 Glucose-6-phosphate isomerase family profile.G6PI_MOUSE7-553
 
  2A:7-553
B:7-553
2P_GLUCOSE_ISOMERASE_1PS00765 Phosphoglucose isomerase signature 1.G6PI_MOUSE268-281
 
  2A:268-281
B:268-281
3P_GLUCOSE_ISOMERASE_2PS00174 Phosphoglucose isomerase signature 2.G6PI_MOUSE502-519
 
  2A:502-519
B:502-519

(-) Exons   (0, 0)

(no "Exon" information available for 2CVP)

(-) 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:557
 aligned with G6PI_MOUSE | P06745 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:557
                                    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       490       500       510       520       530       540       550       
           G6PI_MOUSE     1 MAALTRNPQFQKLLEWHRANSANLKLRELFEADPERFNNFSLNLNTNHGHILVDYSKNLVNKEVMQMLVELAKSRGVEAARDNMFSGSKINYTENRAVLHVALRNRSNTPIKVDGKDVMPEVNRVLDKMKSFCQRVRSGDWKGYTGKSITDIINIGIGGSDLGPLMVTEALKPYSKGGPRVWFVSNIDGTHIAKTLASLSPETSLFIIASKTFTTQETITNAETAKEWFLEAAKDPSAVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDHFEQLLSGAHWMDQHFLKTPLEKNAPVLLALLGIWYINCYGCETHALLPYDQYMHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKLPEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGIMWDINSFDQWGVELGKQLAKKIEPELEGSSAVTSHDSSTNGLISFIKQQRDTKL 557
               SCOP domains d2cvpa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2cvpA01 A:1-99,A:295-515 Glucose-6-phosphate isomerase like protein; domain 1                      2cvpA02 A:100-294 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                             2cvpA01 A:1-99,A:295-515 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                                                2cvpA03 A:516-556                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhheeeee....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhhh.......ee..eehhhhhhhhhhhhhhhhhhhhh............eeeee.hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhh......eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeee.hhhhhhhhh.hhh.eee.....hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhh................eee......hhhhhhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------P_GLUCOSE_ISOMERASE_3  PDB: A:7-553 UniProt: 7-553                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ---- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOMERAS-------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cvp A   1 MAALTRNPQFQKLLEWHRANSANLKLRELFEADPERFNNFSLNLNTNHGHILVDYSKNLVSKEVMQMLVELAKSRGVEAARDNMFSGSKINYTEDRAVLHVALRNRSNTPIKVDGKDVMPEVNRVLDKMKSFCQRVRSGDWKGYTGKSITDIINIGIGGSDLGPLMVTEALKPYSKGGPRVWFVSNIDGTHIAKTLASLSPETSLFIIASKTFTTQETITNAETAKEWFLEAAKDPSAVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDHFEQLLSGAHWMDQHFLKTPLEKNAPVLLALLGIWYINCYGCETHALLPYDQYMHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKLPEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGIMWDINSFDQWGVELGKQLAKKIEPELEGSSAVTSHDSSTNGLISFIKQQRDTKL 557
                                    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       490       500       510       520       530       540       550       

Chain B from PDB  Type:PROTEIN  Length:557
 aligned with G6PI_MOUSE | P06745 from UniProtKB/Swiss-Prot  Length:558

    Alignment length:557
                                    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       490       500       510       520       530       540       550       
           G6PI_MOUSE     1 MAALTRNPQFQKLLEWHRANSANLKLRELFEADPERFNNFSLNLNTNHGHILVDYSKNLVNKEVMQMLVELAKSRGVEAARDNMFSGSKINYTENRAVLHVALRNRSNTPIKVDGKDVMPEVNRVLDKMKSFCQRVRSGDWKGYTGKSITDIINIGIGGSDLGPLMVTEALKPYSKGGPRVWFVSNIDGTHIAKTLASLSPETSLFIIASKTFTTQETITNAETAKEWFLEAAKDPSAVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDHFEQLLSGAHWMDQHFLKTPLEKNAPVLLALLGIWYINCYGCETHALLPYDQYMHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKLPEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGIMWDINSFDQWGVELGKQLAKKIEPELEGSSAVTSHDSSTNGLISFIKQQRDTKL 557
               SCOP domains d2cvpb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2cvpB01 B:1-99,B:295-515 Glucose-6-phosphate isomerase like protein; domain 1                      2cvpB02 B:100-294 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                             2cvpB01 B:1-99,B:295-515 Glucose-6-phosphate isomerase like protein; domain 1                                                                                                                                                2cvpB03 B:516-556                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhheeeee....eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh.......ee..eehhhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhh.....eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhheeee..hhhhhhhhh.hhh.ee......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhhh................eee....hhhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhhhh......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------P_GLUCOSE_ISOMERASE_3  PDB: B:7-553 UniProt: 7-553                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ---- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOM----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------P_GLUCOSE_ISOMERAS-------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cvp B   1 MAALTRNPQFQKLLEWHRANSANLKLRELFEADPERFNNFSLNLNTNHGHILVDYSKNLVSKEVMQMLVELAKSRGVEAARDNMFSGSKINYTEDRAVLHVALRNRSNTPIKVDGKDVMPEVNRVLDKMKSFCQRVRSGDWKGYTGKSITDIINIGIGGSDLGPLMVTEALKPYSKGGPRVWFVSNIDGTHIAKTLASLSPETSLFIIASKTFTTQETITNAETAKEWFLEAAKDPSAVAKHFVALSTNTAKVKEFGIDPQNMFEFWDWVGGRYSLWSAIGLSIALHVGFDHFEQLLSGAHWMDQHFLKTPLEKNAPVLLALLGIWYINCYGCETHALLPYDQYMHRFAAYFQQGDMESNGKYITKSGARVDHQTGPIVWGEPGTNGQHAFYQLIHQGTKMIPCDFLIPVQTQHPIRKGLHHKILLANFLAQTEALMKGKLPEEARKELQAAGKSPEDLEKLLPHKVFEGNRPTNSIVFTKLTPFILGALIAMYEHKIFVQGIMWDINSFDQWGVELGKQLAKKIEPELEGSSAVTSHDSSTNGLISFIKQQRDTKL 557
                                    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       490       500       510       520       530       540       550       

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G6PI_MOUSE | P06745)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0004347    glucose-6-phosphate isomerase activity    Catalysis of the reaction: D-glucose 6-phosphate = D-fructose 6-phosphate.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0016866    intramolecular transferase activity    Catalysis of the transfer of a functional group from one position to another within a single molecule.
    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:0048029    monosaccharide binding    Interacting selectively and non-covalently with any monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0046185    aldehyde catabolic process    The chemical reactions and pathways resulting in the breakdown of aldehydes, any organic compound with the formula R-CH=O.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    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:0034101    erythrocyte homeostasis    Any process of regulating the production and elimination of erythrocytes within an organism.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0051156    glucose 6-phosphate metabolic process    The chemical reactions and pathways involving glucose 6-phosphate, a monophosphorylated derivative of glucose with the phosphate group attached to C-6.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0061620    glycolytic process through glucose-6-phosphate    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, occurring through a glucose-6-phosphate intermediate, with the concomitant production of a small amount of ATP.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0007611    learning or memory    The acquisition and processing of information and/or the storage and retrieval of this information over time.
    GO:0001707    mesoderm formation    The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
    GO:0019242    methylglyoxal biosynthetic process    The chemical reactions and pathways resulting in the formation of methylglyoxal, CH3-CO-CHO, the aldehyde of pyruvic acid.
    GO:0043154    negative regulation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
cellular component
    GO:0060170    ciliary membrane    The portion of the plasma membrane surrounding a cilium.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        G6PI_MOUSE | P067451u0e 1u0f 1u0g 2cxn 2cxo 2cxp 2cxq 2cxr 2cxs 2cxt 2cxu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2CVP)