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Title :   CRYSTAL STRUCTURE OF HUMAN GAMMA-BUTYROBETAINE,2-OXOGLUTARATE IN COMPLEX WITH 449, A NOVEL SUBSTRATE

Authors :   M. A. Mcdonough, G. Kochan, A. Rydzik, C. J. Schofield

Date :   02 Apr 14 (Deposition) - 17 Sep 14 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Oxidoreductase, 2-Og And Iron Dependent Dioxygenase, Carnitine Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Rydzik, I. K. H. Leung, G. T. Kochan, M. A. Mcdonough, T. D. W. Claridge, C. J. Schofield
Oxygenase-Catalyzed Desymmetrization Of N, N-Dialkyl-Piperidine-4-Carboxylic Acids.
Angew. Chem. Int. Ed. Engl. V. 53 10925 2014
PubMed-ID: 25164544 | Reference-DOI: 10.1002/ANIE.201406125

Molecule 1 - GAMMA-BUTYROBETAINE DIOXYGENASE
	Chains	:	A
	EC Number	:	1.14.11.1
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Common	:	CABBAGE LOOPER
	Expression System Plasmid	:	PFBOH-LIC-BSE
	Expression System Strain	:	DH10BAC
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GAMMA-BUTYROBETAINE HYDROXYLASE, GAMMA-BBH, GAMMA- BUTYROBETAINE, 2-OXOGLUTARATE DIOXYGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 5)

No.	Name	Count	Type	Full Name
1	449	1	Ligand/Ion	4-CARBOXY-1,1-DIMETHYLPIPERIDIN-1-IUM
2	NI	1	Ligand/Ion	NICKEL (II) ION
3	OGA	1	Ligand/Ion	N-OXALYLGLYCINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	449	2	Ligand/Ion	4-CARBOXY-1,1-DIMETHYLPIPERIDIN-1-IUM
2	NI	-1	Ligand/Ion	NICKEL (II) ION
3	OGA	2	Ligand/Ion	N-OXALYLGLYCINE
4	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:202 , ASP A:204 , HIS A:347 , OGA A:1386 , HOH A:2274	BINDING SITE FOR RESIDUE NI A 388
2	AC2	SOFTWARE	CYS A:38 , CYS A:40 , CYS A:43 , HIS A:82	BINDING SITE FOR RESIDUE ZN A 389
3	AC3	SOFTWARE	TYR A:177 , TRP A:181 , ASN A:191 , TYR A:194 , ASP A:204 , TYR A:205 , ASN A:292 , THR A:295 , TYR A:366 , OGA A:1386 , HOH A:2260 , HOH A:2276 , HOH A:2330	BINDING SITE FOR RESIDUE 449 A 1385
4	AC4	SOFTWARE	VAL A:183 , ALA A:193 , HIS A:202 , ASP A:204 , HIS A:347 , ARG A:349 , ARG A:360 , LEU A:362 , NI A:388 , 449 A:1385 , HOH A:2274 , HOH A:2296	BINDING SITE FOR RESIDUE OGA A 1386
5	AC5	SOFTWARE	ASP A:70 , TYR A:75 , TYR A:83 , HOH A:2124	BINDING SITE FOR RESIDUE PEG A 1387

(no "SS Bond" information available for 4CWD)

(no "Cis Peptide Bond" information available for 4CWD)

(no "SAP(SNP)/Variant" information available for 4CWD)

(no "PROSITE Motif" information available for 4CWD)

(no "Exon" information available for 4CWD)

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
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Chain A from PDB  Type:PROTEIN  Length:385
 aligned with BODG_HUMAN | O75936 from UniProtKB/Swiss-Prot  Length:387

    Alignment length:385
                             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     - -MACTIQKAEALDGAHLMQILWYDEEESLYPAVWLRDNCPCSDCYLDSAKARKLLVEALDVNIGIKGLIFDRKKVYITWPDEHYSEFQADWLKKRCFSKQARAKLQRELFFPECQYWGSELQLPTLDFEDVLRYDEHAYKWLSTLKKVGIVRLTGASDKPGEVSKLGKRMGFLYLTFYGHTWQVQDKIDANNVAYTTGKLSFHTDYPALHHPPGVQLLHCIKQTVTGGDSEIVDGFNVCQKLKKNNPQAFQILSSTFVDFTDIGVDYCDFSVQSKHKIIELDDKGQVVRINFNNATRDTIFDVPVERVQPFYAALKEFVDLMNSKESKFTFKMNPGDVITFDNWRLLHGRRSYEAGTEISRHLEGAYADWDVVMSRLRILRQRVE 384
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeee....eeeeee....eeeeehhhhhhh......ee....ee..hhhhh.......eeee...eeeee.....eeeeehhhhhhh..hhhhhhhhhhhhhh.............eeehhhhhhhhhhhhhhhhhhhhhheeeee......hhhhhhhhhhh..........eee.......hhhhh...eeee...........eeeeeeee.......eeeeehhhhhhhhhhhhhhhhhhhh..eeeeeeeee...eeeeeeeee.eee.....eeee.............hhhhhhhhhhhhhhhhhhhhh....eee......eeeee...eeeee...........eeeeeeehhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cwd A   0 SMACTIQKAEALDGAHLMQILWYDEEESLYPAVWLRDNCPCSDCYLDSAKARKLLVEALDVNIGIKGLIFDRKKVYITWPDEHYSEFQADWLKKRCFSKQARAKLQRELFFPECQYWGSELQLPTLDFEDVLRYDEHAYKWLSTLKKVGIVRLTGASDKPGEVSKLGKRMGFLYLTFYGHTWQVQDKIDANNVAYTTGKLSFHTDYPALHHPPGVQLLHCIKQTVTGGDSEIVDGFNVCQKLKKNNPQAFQILSSTFVDFTDIGVDYCDFSVQSKHKIIELDDKGQVVRINFNNATRDTIFDVPVERVQPFYAALKEFVDLMNSKESKFTFKMNPGDVITFDNWRLLHGRRSYEAGTEISRHLEGAYADWDVVMSRLRILRQRVE 384
                                     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

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 '\|'

(no "SCOP Domain" information available for 4CWD)

(no "CATH Domain" information available for 4CWD)

(no "Pfam Domain" information available for 4CWD)

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		449	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NI	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		OGA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4cwd)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	4cwd
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	1.14.11.1
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	BODG_HUMAN \| O75936	:	3ms5 3n6w 3o2g 4bg1 4bgk 4bgm 4bhf 4bhg 4bhi 4c5w 4c8r

(no "Related Entries Specified in the PDB File" available for 4CWD)

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Ligands, Modified Residues, Ions (5, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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