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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GLUTAMINASE IN COMPLEX WITH INHIBITOR 2
 
Authors :  K. Thangavelu, J. Sivaraman
Date :  23 Feb 12  (Deposition) - 13 Jun 12  (Release) - 27 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Thangavelu, C. Q. Pan, T. Karlberg, G. Balaji, M. Uttamchandani, V. Suresh, H. Schuler, B. C. Low, J. Sivaraman
Structural Basis For The Allosteric Inhibitory Mechanism Of Human Kidney-Type Glutaminase (Kga) And Its Regulation By Raf-Mek-Erk Signaling In Cancer Cell Metabolism.
Proc. Natl. Acad. Sci. Usa V. 109 7705 2012
PubMed-ID: 22538822  |  Reference-DOI: 10.1073/PNAS.1116573109

(-) Compounds

Molecule 1 - GLUTAMINASE KIDNEY ISOFORM, MITOCHONDRIAL
    ChainsA
    EC Number3.5.1.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 221-533
    GeneGLS, GLS1, KIAA0838
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymGLS, K-GLUTAMINASE, L-GLUTAMINE AMIDOHYDROLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1BP01Ligand/Ion5,5'-(SULFANEDIYLDIETHANE-2,1-DIYL)BIS(1,3,4-THIADIAZOL-2-AMINE)
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1BP04Ligand/Ion5,5'-(SULFANEDIYLDIETHANE-2,1-DIYL)BIS(1,3,4-THIADIAZOL-2-AMINE)
2SO44Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:319 , PHE A:322 , LEU A:323 , TYR A:394BINDING SITE FOR RESIDUE BP0 A 601
2AC2SOFTWAREPHE A:373 , SER A:374 , ASN A:375 , ALA A:376 , HOH A:732 , HOH A:734BINDING SITE FOR RESIDUE SO4 A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VP2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VP2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049188A254PGLSK_HUMANPolymorphism16833035AA254P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049188A254PGLSK_HUMANPolymorphism16833035AA254P

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VP2)

(-) Exons   (0, 0)

(no "Exon" information available for 3VP2)

(-) 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:311
 aligned with GLSK_HUMAN | O94925 from UniProtKB/Swiss-Prot  Length:669

    Alignment length:313
                                   228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528   
           GLSK_HUMAN   219 FVIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGLRFNKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYD 531
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhh....ee...hhhhhh......eeeeee....eeeee.....ee...hhhhhhhhhhhhhhhhhhhh..........--...............hhhhhhhhhh......hhhhhhhhhhhhhhhhh.....eehhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhhhhhhhhheeehhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee...eeeeee..ee.....hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -----------------------------------P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vp2 A 219 SMIPDFMSFTSHIDELYESAKKQSGGKVADYIPQLAKFSPDLWGVSVCTVDGQRHSTGDTKVPFCLQSCVKPLKYAIAVNDLGTEYVHRYVGKEPSGL--NKLFLNEDDKPHNPMVNAGAIVVTSLIKQGVNNAEKFDYVMQFLNKMAGNEYVGFSNATFQSERESGDRNFAIGYYLKEKKCFPEGTDMVGILDFYFQLCSIEVTCESASVMAATLANGGFCPITGERVLSPEAVRNTLSLMHSCGMYDFSGQFAFHVGLPAKSGVAGGILLVVPNVMGMMCWSPPLDKMGNSVKGIHFCHDLVSLCNFHNYD 531
                                   228       238       248       258       268       278       288       298       308       | -|      328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528   
                                                                                                                           316  |                                                                                                                                                                                                                    
                                                                                                                              319                                                                                                                                                                                                                    

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3VP2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VP2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VP2)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (GLSK_HUMAN | O94925)
molecular function
    GO:0004359    glutaminase activity    Catalysis of the reaction: L-glutamine + H2O = L-glutamate + NH3.
    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: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:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0006537    glutamate biosynthetic process    The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.
    GO:0014047    glutamate secretion    The controlled release of glutamate by a cell. The glutamate is the most abundant excitatory neurotransmitter in the nervous system.
    GO:0006543    glutamine catabolic process    The chemical reactions and pathways resulting in the breakdown of glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0051289    protein homotetramerization    The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
    GO:0002087    regulation of respiratory gaseous exchange by neurological system process    A process carried out by the nervous system that is required for the proper control of respiratory gaseous exchange. This process occurs in the respiratory center of the brain in vertebrates.
    GO:0001967    suckling behavior    Specific behavior of a newborn or infant mammal that results in the derivation of nourishment from the breast.
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:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLSK_HUMAN | O949253czd 3unw 3uo9 3voy 3voz 3vp0 3vp1 3vp3 3vp4 4o7d 5d3o 5fi2 5fi6 5fi7 5hl1 5i94 5jyo 5jyp 5u0i 5u0j 5uqe

(-) Related Entries Specified in the PDB File

3voy 3vp0 3vp1 3vp3 3vp4 3vpz