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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE HYDROXYLASE
 
Authors :  J. Rumnieks, A. Zeltins, A. Leonchiks, A. Kazaks, S. Kotelovica, K. Tar
Date :  26 May 10  (Deposition) - 21 Jul 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Gamma-Butyrobetaine Hydroxylase, Bbh, Dioxygenase, Carnitine, Hydrolase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tars, J. Rumnieks, A. Zeltins, A. Kazaks, S. Kotelovica, A. Leonciks, J. Sharipo, A. Viksna, J. Kuka, E. Liepinsh, M. Dambrova
Crystal Structure Of Human Gamma-Butyrobetaine Hydroxylase.
Biochem. Biophys. Res. Commun. V. 398 634 2010
PubMed-ID: 20599753  |  Reference-DOI: 10.1016/J.BBRC.2010.06.121

(-) Compounds

Molecule 1 - GAMMA-BUTYROBETAINE DIOXYGENASE
    Chains: A
    EC Number: 1.14.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: WK6
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BBH, BBOX, BBOX1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GAMMA-BUTYROBETAINE,2-OXOGLUTARATE DIOXYGENASE, GAMMA- BUTYROBETAINE HYDROXYLASE, GAMMA-BBH

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:38 , CYS A:40 , CYS A:43 , HIS A:82BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREASN A:245 , PRO A:246 , GLN A:247 , ALA A:248 , GLU A:316 , HOH A:561BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWARELEU A:45 , ASP A:46 , SER A:47 , CYS A:267 , ASP A:268 , ARG A:375 , ARG A:382BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWARELYS A:93 , ARG A:94BINDING SITE FOR RESIDUE SO4 A 404
5AC5SOFTWAREARG A:101 , PRO A:303 , HOH A:677BINDING SITE FOR RESIDUE SO4 A 405
6AC6SOFTWARELYS A:52 , LYS A:167 , ARG A:168 , HOH A:653BINDING SITE FOR RESIDUE SO4 A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3N6W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3N6W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3N6W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3N6W)

(-) Exons   (0, 0)

(no "Exon" information available for 3N6W)

(-) 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:360
 aligned with BODG_HUMAN | O75936 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:386
                             1                                                                                                                                                                                                                                                                                                                                                                                                
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379      
           BODG_HUMAN     - -MACTIQKAEALDGAHLMQILWYDEEESLYPAVWLRDNCPCSDCYLDSAKARKLLVEALDVNIGIKGLIFDRKKVYITWPDEHYSEFQADWLKKRCFSKQARAKLQRELFFPECQYWGSELQLPTLDFEDVLRYDEHAYKWLSTLKKVGIVRLTGASDKPGEVSKLGKRMGFLYLTFYGHTWQVQDKIDANNVAYTTGKLSFHTDYPALHHPPGVQLLHCIKQTVTGGDSEIVDGFNVCQKLKKNNPQAFQILSSTFVDFTDIGVDYCDFSVQSKHKIIELDDKGQVVRINFNNATRDTIFDVPVERVQPFYAALKEFVDLMNSKESKFTFKMNPGDVITFDNWRLLHGRRSYEAGTEISRHLEGAYADWDVVMSRLRILRQRVEN 385
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------DUF971-3n6wA02 A:7-67                                        ----------------------------------------TauD-3n6wA01 A:108-366                                                                                                                                                                                                                                             ------------------- Pfam domains
         Sec.struct. author .....eeeeeee....eeeeee....eeeeehhhhhhh......ee....ee..hhhhh.......eeee...eeeee.....eeeeehhhhhhh..hhhhhhhhhhhhhh.............eeehhhhhhhhhhhhhhhhhhhhhheeeee......hhhhhhhhhhh.............ee.------------...............eeeeee...-----.eeeeehhhhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeee.eee.....eeee.............hhhhhhhhhhhhhhhhhhhh.....eee......eeeee...eeee..---------..eeeeeehhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n6w A   0 SMACTIQKAEALDGAHLMQILWYDEEESLYPAVWLRDNCPCSDCYLDSAKARKLLVEALDVNIGIKGLIFDRKKVYITWPDEHYSEFQADWLKKRCFSKQARAKLQRELFFPECQYWGSELQLPTLDFEDVLRYDEHAYKWLSTLKKVGIVRLTGASDKPGEVSKLGKRMGFLYLTFYGHTWQVQDK------------LSFHTDYPALHHPPGVQLLHCIKQ-----DSEIVDGFNVCQKLKKNNPQAFQILSSTFVDFTDIGVDYCDFSVQSKHKIIELDDKGQVVRINFNNATRDTIFDVPVERVQPFYAALKEFVDLMNSKESKFTFKMNPGDVITFDNWRLLHGRR---------RHLEGAYADWDVVMSRLRILRQRVEN 385
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179      |  -       199       209       219  |    229       239       249       259       269       279       289       299       309       319       329       339       349|        -|      369       379      
                                                                                                                                                                                                                    186          199                    222   228                                                                                                                       350       360
   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 3N6W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3N6W)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Cupin (179)
(-)
Clan: no clan defined [family: DUF971] (5)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (BODG_HUMAN | O75936)
molecular function
    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:0008336    gamma-butyrobetaine dioxygenase activity    Catalysis of the reaction: 2-oxoglutarate + 4-(trimethylammonio)butanoate + O(2) = carnitine + CO(2) + succinate.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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: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:0045329    carnitine biosynthetic process    The chemical reactions and pathways resulting in the formation of carnitine (hydroxy-trimethyl aminobutyric acid), a compound that participates in the transfer of acyl groups across the inner mitochondrial membrane.
    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: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: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

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UniProtKB/Swiss-Prot
        BODG_HUMAN | O75936: 3ms5 3o2g 4bg1 4bgk 4bgm 4bhf 4bhg 4bhi 4c5w 4c8r 4cwd

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