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(-) Description

Authors :  K. L. Kavanagh, M. A. Mcdonough, T. Searles, D. Butler, G. Bunkoczi, F. V A. Edwards, C. Arrowsmith, M. Sundstrom, C. J. Schofield, U. Opperman Structural Genomics Consortium (Sgc)
Date :  21 Jun 05  (Deposition) - 16 Aug 05  (Release) - 13 Jul 11  (Revision)
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Jelly Roll, Double-Stranded Beta-Helix, Structural Genomics, Structural Genomics Consortium, Sgc, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  M. A. Mcdonough, K. L. Kavanagh, D. Butler, T. Searles, U. Oppermann, C. J. Schofield
Structure Of Human Phytanoyl-Coa 2-Hydroxylase Identifies Molecular Mechanisms Of Refsum Disease
J. Biol. Chem. V. 280 41101 2005
PubMed-ID: 16186124  |  Reference-DOI: 10.1074/JBC.M507528200

(-) Compounds

    EC Number1.14.11.18
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET24A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GenePHYH, PAHX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
2FE21Ligand/IonFE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
2AC2SOFTWARELYS A:120 , MET A:157 , ILE A:159 , HIS A:175 , ASP A:177 , TRP A:193 , HIS A:264 , SER A:266 , ARG A:275 , FE2 A:450 , HOH A:463BINDING SITE FOR RESIDUE AKG A 451

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A1X)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Arg A:184 -Pro A:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (16, 16)

Asymmetric/Biological Unit (16, 16)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_018619N83YPAHX_HUMANDisease (RD)  ---AN83Y
02UniProtVAR_017483P173SPAHX_HUMANDisease (RD)  ---AP173S
03UniProtVAR_018631H175RPAHX_HUMANDisease (RD)  ---AH175R
04UniProtVAR_017484Q176KPAHX_HUMANDisease (RD)28939672AQ176K
05UniProtVAR_017485D177GPAHX_HUMANDisease (RD)770262329AD177G
06UniProtVAR_017486W193RPAHX_HUMANDisease (RD)  ---AW193R
07UniProtVAR_017487E197QPAHX_HUMANDisease (RD)  ---AE197Q
08UniProtVAR_017488I199FPAHX_HUMANDisease (RD)  ---AI199F
09UniProtVAR_017489G204SPAHX_HUMANDisease (RD)28939673AG204S
11UniProtVAR_017490H220YPAHX_HUMANDisease (RD)767216891AH220Y
13UniProtVAR_017492F257SPAHX_HUMANDisease (RD)  ---AF257S
14UniProtVAR_005525N269HPAHX_HUMANDisease (RD)104894179AN269H
15UniProtVAR_017493R275QPAHX_HUMANDisease (RD)28939674AR275Q
16UniProtVAR_005526R275WPAHX_HUMANDisease (RD)28939671AR275W

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A1X)

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5aENST000002630385aENSE00001629825chr10:13337606-13337496111PAHX_HUMAN45-82381A:45-82 (gaps)38
1.6bENST000002630386bENSE00001650856chr10:13336596-13336428169PAHX_HUMAN82-138571A:82-138 (gaps)57
1.9ENST000002630389ENSE00002153198chr10:13325839-13325690150PAHX_HUMAN227-276501A:234-276 (gaps)43
1.10ENST0000026303810ENSE00000915175chr10:13323110-13322976135PAHX_HUMAN277-321451A:277-321 (gaps)45

(-) 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:253
 aligned with PAHX_HUMAN | O14832 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:296
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332      
               SCOP domains d2a1xa1   A:43-338 Phytanoyl-CoA dioxygenase, PhyH                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------Y-----------------------------------------------------------------------------------------S-RKG---------------R---Q-F----S----------S----Y------------------------Q-----------S-----------H-----Q--------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W--------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.4------------------------------------Exon 1.6b  PDB: A:82-138 (gaps) UniProt: 82-138          Exon 1.7a  PDB: A:139-164   ------------------------------------------------------------Exon 1.9  PDB: A:234-276 (gaps) UniProt: 227-276  Exon 1.10  PDB: A:277-321 (gaps)             Exon 1.11b        Transcript 1 (1)
           Transcript 1 (2) --Exon 1.5a  PDB: A:45-82 (gaps)        -----------------------------------------------------------------------------------Exon 1.8b  PDB: A:173-222 UniProt: 166-226 [INCOMPLETE]      ---------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                                   | -|       62        72        82        92       102     |   - |     122       132       142       152       162 |       -|      182       192       202       212       222         - |   | 242       252       262       272       282       292       302         -      |322       332      
                                  50 53                                                    108   114                                               164      173                                              222         234 238 |                                                           302              319                   

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2A1X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A1X)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PAHX_HUMAN | O14832)
molecular function
    GO:0031418    L-ascorbic acid binding    Interacting selectively and non-covalently with L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0048244    phytanoyl-CoA dioxygenase activity    Catalysis of the reaction: 2-oxoglutarate + O(2) + phytanoyl-CoA = 2-hydroxyphytanoyl-CoA + CO(2) + succinate.
    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:0001561    fatty acid alpha-oxidation    A metabolic pathway by which 3-methyl branched fatty acids are degraded. These compounds are not degraded by the normal peroxisomal beta-oxidation pathway, because the 3-methyl blocks the dehydrogenation of the hydroxyl group by hydroxyacyl-CoA dehydrogenase. The 3-methyl branched fatty acid is converted in several steps to pristenic acid, which can then feed into the beta-oxidative pathway.
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0006720    isoprenoid metabolic process    The chemical reactions and pathways involving isoprenoid compounds, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
    GO:0097089    methyl-branched fatty acid metabolic process    The chemical reactions and pathways involving methyl-branched fatty acids, aliphatic monocarboxylic acids with methyl branches on the main chain.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    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.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.


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 Related Entries

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

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(-) Related Entries Specified in the PDB File

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