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(-) Description

Title :  THE CRYSTAL STRUCTURE OF HUMAN ALPHA-AMINO-BETA-CARBOXYMUCONATE-EPSILON-SEMIALDEHYDE DECARBOXYLASE IN COMPLEX WITH 1,3- DIHYDROXYACETONEPHOSPHATE SUGGESTS A REGULATORY LINK BETWEEN NAD SYNTHESIS AND GLYCOLYSIS
 
Authors :  S. Garavaglia, S. Perozzi, L. Galeazzi, N. Raffaelli, M. Rizzi
Date :  29 Jun 09  (Deposition) - 03 Nov 09  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Neurological Disorders, Metal-Dependent Amidohydrolase, Kynurenine Pathway, Alternative Splicing, Quinolinic Acid, Nad Biosynthesis, Cerebral Malaria, Lyase, Decarboxylase, Picolinic Acid, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Garavaglia, S. Perozzi, L. Galeazzi, N. Raffaelli, M. Rizzi
The Crystal Structure Of Human Alpha-Amino-Beta- Carboxymuconate-Epsilon-Semialdehyde Decarboxylase In Complex With 1, 3-Dihydroxyacetonephosphate Suggests A Regulatory Link Between Nad Synthesis And Glycolysis
Febs J. V. 276 6615 2009
PubMed-ID: 19843166  |  Reference-DOI: 10.1111/J.1742-4658.2009.07372.X

(-) Compounds

Molecule 1 - 2-AMINO-3-CARBOXYMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE
    ChainsA
    EC Number4.1.1.45
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System Cell LineGS115
    Expression System Taxid4922
    Expression System VectorPHIL-D2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymALPHA-AMINO-BETA-CARBOXYMUCONATE-EPSILON- SEMIALDEHYDE DECARBOXYLASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
113P1Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2GOL1Ligand/IonGLYCEROL
3ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
113P2Ligand/Ion1,3-DIHYDROXYACETONEPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:6 , HIS A:8 , HIS A:174 , ASP A:291 , HOH A:2215BINDING SITE FOR RESIDUE ZN A1333
2AC2SOFTWAREARG A:47 , PRO A:77 , HIS A:174 , TRP A:191 , ASP A:291 , PHE A:294 , LEU A:296 , HOH A:2127 , HOH A:2215 , HOH A:2216BINDING SITE FOR RESIDUE 13P A1334
3AC3SOFTWAREVAL A:147 , ASN A:148 , GLU A:149 , HOH A:2095BINDING SITE FOR RESIDUE GOL A1335

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WM1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:292 -Pro A:293

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WM1)

(-) Exons   (0, 0)

(no "Exon" information available for 2WM1)

(-) 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:332
 aligned with ACMSD_HUMAN | Q8TDX5 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:332
                                    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  
          ACMSD_HUMAN     1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRIREMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQAPELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQMDGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELEPGKLIESMEEFDEETKNKLKAGNALAFLGLER 332
               SCOP domains d2wm1a_ A: automated matches                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Amidohydro_2-2wm1A01 A:3-330                                                                                                                                                                                                                                                                                                            -- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhh....eeeeeee..eeeeee..eeeeeee.hhhhhhhhhhhhhhhh..eeeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee.ee..ee..hhhhhhhhhhhhhhh.eeeee......hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eee.hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...eee....hhhhhhhhhhhhh...ee..............hhhhhh....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wm1 A   1 MKIDIHSHILPKEWPDLKKRFGYGGWVQLQHHSKGEAKLLKDGKVFRVVRENCWDPEVRIREMDQKGVTVQALSTVPVMFSYWAKPEDTLNLCQLLNNDLASTVVSYPRRFVGLGTLPMQAPELAVKEMERCVKELGFPGVQIGTHVNEWDLNAQELFPVYAAAERLKCSLFVHPWDMQMDGRMAKYWLPWLVGMPAETTIAICSMIMGGVFEKFPKLKVCFAHGGGAFPFTVGRISHGFSMRPDLCAQDNPMNPKKYLGSFYTDALVHDPLSLKLLTDVIGKDKVILGTDYPFPLGELEPGKLIESMEEFDEETKNKLKAGNALAFLGLER 332
                                    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  

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  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 2WM1)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A   (ACMSD_HUMAN | Q8TDX5)
molecular function
    GO:0001760    aminocarboxymuconate-semialdehyde decarboxylase activity    Catalysis of the reaction: 2-amino-3-carboxymuconate 6-semialdehyde + H(+) = 2-aminomuconate 6-semialdehyde + CO(2).
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:1905004    picolinic acid biosynthetic process    The chemical reactions and pathways resulting in the formation of picolinic acid.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0046874    quinolinate metabolic process    The chemical reactions and pathways involving quinolinate, the anion of quinolinic acid, also known as 2,3-pyridinedicarboxylic acid.
    GO:1905012    regulation of 'de novo' NAD biosynthetic process from tryptophan    Any process that modulates the frequency, rate or extent of 'de novo' NAD biosynthetic process from tryptophan.
    GO:1904984    regulation of quinolinate biosynthetic process    Any process that modulates the frequency, rate or extent of quinolinate biosynthetic process.
    GO:0006569    tryptophan catabolic process    The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.
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)

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        ACMSD_HUMAN | Q8TDX54igm 4ign 4ih3 4ofc

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