Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  GLUTAMINASE SUBUNIT OF THE PLASMODIAL PLP SYNTHASE (VITAMIN B6 BIOSYNTHESIS)
 
Authors :  M. Gengenbacher, T. B. Fitzpatrick, T. Raschle, K. Flicker, I. Sinning S. Mueller, P. Macheroux, I. Tews, B. Kappes
Date :  17 Jul 05  (Deposition) - 10 Jan 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glutaminase, Plp-Synthase, Vitamin B6, Malaria, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Gengenbacher, T. B. Fitzpatrick, T. Raschle, K. Flicker, I. Sinning, S. Mueller, P. Macheroux, I. Tews, B. Kappes
Vitamin B6 Biosynthesis By The Malaria Parasite Plasmodium Falciparum: Biochemical And Structural Insights
J. Biol. Chem. V. 281 3633 2006
PubMed-ID: 16339145  |  Reference-DOI: 10.1074/JBC.M508696200

(-) Compounds

Molecule 1 - PDX2 PROTEIN
    ChainsA, B
    EC Number2.6.-.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21A(+)
    Expression System StrainBL21(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GenePDX2
    Organism CommonMALARIA PARASITE P. FALCIPARUM
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid5833
    SynonymGLUTAMINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1PG4-1Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:136 , THR A:171 , SER A:173 , ASN A:180 , HOH A:1164 , LEU B:11BINDING SITE FOR RESIDUE PG4 A 1101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:122 -Phe A:123

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDXT_SNO_2PS51130 PdxT/SNO family profile.PDX2_PLAF75-214
 
  2A:5-214
B:5-214
2PDXT_SNO_1PS01236 PdxT/SNO family family signature.PDX2_PLAF746-56
 
  2A:46-56
B:46-56
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDXT_SNO_2PS51130 PdxT/SNO family profile.PDX2_PLAF75-214
 
  1A:5-214
-
2PDXT_SNO_1PS01236 PdxT/SNO family family signature.PDX2_PLAF746-56
 
  1A:46-56
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDXT_SNO_2PS51130 PdxT/SNO family profile.PDX2_PLAF75-214
 
  1-
B:5-214
2PDXT_SNO_1PS01236 PdxT/SNO family family signature.PDX2_PLAF746-56
 
  1-
B:46-56

(-) Exons   (0, 0)

(no "Exon" information available for 2ABW)

(-) 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:216
 aligned with PDX2_PLAF7 | Q8IIK4 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:220
                                                                                                                                                                                                                                                   219  
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       | -
           PDX2_PLAF7     2 SEITIGVLSLQGDFEPHINHFIKLQIPSLNIIQVRNVHDLGLCDGLVIPGGESTTVRRCCAYENDTLYNALVHFIHVLKKPIWGTCAGCILLSKNVENIKLYSNFGNKFSFGGLDITICRNFYGSQNDSFICSLNIISDSSAFKKDLTAACIRAPYIREILSDEVKVLATFSHESYGPNIIAAVEQNNCLGTVFHPELLPHTAFQQYFYEKVKNYKYS--   -
               SCOP domains d2abwa1 A:2-219 Pyridoxine biosynthesis protein 2, Pdx2                                                                                                                                                                   -- SCOP domains
               CATH domains 2abwA00 A:2-221  [code=3.40.50.880, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhh.....eeeeee.hhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhheeeee.......hhhhh....eeeeee...----..eeeee.ee...........eeeee...eeeee.....eeeeeeee...eeeeeeeeee..eeee..hhhhh..hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PDXT_SNO_2  PDB: A:5-214 UniProt: 5-214                                                                                                                                                                           ------- PROSITE (1)
                PROSITE (2) --------------------------------------------PDXT_SNO_1 --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2abw A   2 SEITIGVLSLQGDFEPHINHFIKLQIPSLNIIQVRNVHDLGLCDGLVIPGGESTTVRRCCAYENDTLYNALVHFIHVLKKPIWGTCAGCILLSKNVENIKLYSNFGNKFSFGGLDITICRNF----NDSFICSLNIISDSSAFKKDLTAACIRAPYIREILSDEVKVLATFSHESYGPNIIAAVEQNNCLGTVFHPELLPHTAFQQYFYEKVKNYKYSLE 221
                                    11        21        31        41        51        61        71        81        91       101       111       121 |    |131       141       151       161       171       181       191       201       211       221
                                                                                                                                                   123  128                                                                                             

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with PDX2_PLAF7 | Q8IIK4 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:226
                                                                                                                                                                                                                                                   219        
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       | -      
           PDX2_PLAF7     2 SEITIGVLSLQGDFEPHINHFIKLQIPSLNIIQVRNVHDLGLCDGLVIPGGESTTVRRCCAYENDTLYNALVHFIHVLKKPIWGTCAGCILLSKNVENIKLYSNFGNKFSFGGLDITICRNFYGSQNDSFICSLNIISDSSAFKKDLTAACIRAPYIREILSDEVKVLATFSHESYGPNIIAAVEQNNCLGTVFHPELLPHTAFQQYFYEKVKNYKYS--------   -
               SCOP domains d2abwb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains 2abwB00 B:2-227  [code=3.40.50.880, no name defined]                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhh.....eeeeee.hhhhhhh..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeehhhhhhheeeee.......hhhhh....eeeeee.........eeeee.ee...........eeeee...eeeee.....eeeeeeee...eeeeeeeeee..eeee.........hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---PDXT_SNO_2  PDB: B:5-214 UniProt: 5-214                                                                                                                                                                           ------------- PROSITE (1)
                PROSITE (2) --------------------------------------------PDXT_SNO_1 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2abw B   2 SEITIGVLSLQGDFEPHINHFIKLQIPSLNIIQVRNVHDLGLCDGLVIPGGESTTVRRCCAYENDTLYNALVHFIHVLKKPIWGTCAGCILLSKNVENIKLYSNFGNKFSFGGLDITICRNFYGSQNDSFICSLNIISDSSAFKKDLTAACIRAPYIREILSDEVKVLATFSHESYGPNIIAAVEQNNCLGTVFHPELLPHTAFQQYFYEKVKNYKYSLEHHHHHH 227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221      

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PDX2_PLAF7 | Q8IIK4)
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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0036381    pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity    Catalysis of the reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate. The reaction occurs in two steps: L-glutamine + H2O = L-glutamate + NH3, and subsequently D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate.
biological process
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
    GO:0008614    pyridoxine metabolic process    The chemical reactions and pathways involving pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate.
    GO:0000304    response to singlet oxygen    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 singlet oxygen stimulus. Singlet oxygen is a dioxygen (O2) molecule in which two 2p electrons have similar spin. Singlet oxygen is more highly reactive than the form in which these electrons are of opposite spin, and it is produced in mutant chloroplasts lacking carotenoids and by leukocytes during metabolic burst.
    GO:0042819    vitamin B6 biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
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:1903600    glutaminase complex    A protein complex which is capable of glutaminase activity.

 Visualization

(-) Interactive Views

Asymmetric 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
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:122 - Phe A:123   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) 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
  2abw
    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
  PDX2_PLAF7 | Q8IIK4
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.6.-.-
    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
  PDX2_PLAF7 | Q8IIK4
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PDX2_PLAF7 | Q8IIK44ads

(-) Related Entries Specified in the PDB File

1r9g BACTERIAL ORTHOLOGUE