1BS1 - JenaLib

Title :   DETHIOBIOTIN SYNTHETASE COMPLEXED WITH DETHIOBIOTIN, ADP , INORGANIC PHOSPHATE AND MAGNESIUM

Authors :   H. Kaeck, J. Sandmark, K. J. Gibson, G. Schneider, Y. Lindqvist

Date :   31 Aug 98 (Deposition) - 13 Jan 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Ligase, Biotin Biosynthesis, Aluminum Flouride, Atp-Binding, Phosphoryl Transfer (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Kack, J. Sandmark, K. J. Gibson, G. Schneider, Y. Lindqvist
Crystal Structure Of Two Quaternary Complexes Of Dethiobiotin Synthetase, Enzyme-Mgadp-Alf3-Diaminopelargoni Acid And Enzyme-Mgadp-Dethiobiotin-Phosphate; Implications For Catalysis.
Protein Sci. V. 7 2560 1998
PubMed-ID: 9865950
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	DAA	1	Ligand/Ion	8-AMINO-7-CARBOXYAMINO-NONANOIC ACID WITH ALUMINUMFLUORIDE
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	DAA	1	Ligand/Ion	8-AMINO-7-CARBOXYAMINO-NONANOIC ACID WITH ALUMINUMFLUORIDE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	DAA	2	Ligand/Ion	8-AMINO-7-CARBOXYAMINO-NONANOIC ACID WITH ALUMINUMFLUORIDE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:16 , ASP A:54 , GLU A:115 , HOH A:444 , ADP A:802 , DAA A:850 , MG A:902	BINDING SITE FOR RESIDUE MG A 901
2	AC2	SOFTWARE	GLU A:12 , HOH A:444 , HOH A:754 , ADP A:802 , HOH A:836 , DAA A:850 , MG A:901	BINDING SITE FOR RESIDUE MG A 902
3	AC3	SOFTWARE	GLU A:12 , VAL A:13 , GLY A:14 , LYS A:15 , THR A:16 , VAL A:17 , GLU A:115 , ASN A:175 , ASP A:176 , PRO A:204 , TRP A:205 , LEU A:206 , PRO A:210 , GLU A:211 , HOH A:444 , HOH A:710 , HOH A:711 , HOH A:714 , HOH A:756 , HOH A:836 , DAA A:850 , MG A:901 , MG A:902	BINDING SITE FOR RESIDUE ADP A 802
4	AC4	SOFTWARE	THR A:11 , LYS A:15 , LYS A:37 , ALA A:40 , SER A:41 , ASP A:54 , PRO A:79 , GLU A:115 , ALA A:117 , GLY A:118 , GLY A:150 , CYS A:151 , ILE A:152 , ASN A:153 , TYR A:187 , HOH A:655 , HOH A:717 , HOH A:754 , ADP A:802 , MG A:901 , MG A:902	BINDING SITE FOR RESIDUE DAA A 850

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

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	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:224
 aligned with BIOD1_ECOLI | P13000 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:224
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221    
          BIOD1_ECOLI     2 SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLLGEIPWLAENPENAATGKYINLALL 225
               SCOP domains d1bs1a_ A: Dethiobiotin synthetase                                                                                                                                                                                               SCOP domains
               CATH domains 1bs1A00 A:1-224 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......hhhhhhhhhhhhhh....eeee..eee...........hhhhhhhh.......hhhh..eee.....hhhhhhhh.....hhhhhhhhhhhhh...eeeee..............hhhhhhhh..eeeeeee....hhhhhhhhhhhhhhh...eeeeeee........hhhhhhhhhhh....eeeee......hhh...hhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bs1 A   1 SKRYFVTGTDTEVGKTVASCALLQAAKAAGYRTAGYKPVASGSEKTPEGLRNSDALALQRNSSLQLDYATVNPYTFAEPTSPHIISAQEGRPIESLVMSAGLRALEQQADWVLVEGAGGWFTPLSDTFTFADWVTQEQLPVILVVGVKLGCINHAMLTAQVIQHAGLTLAGWVANDVTPPGKRHAEYMTTLTRMIPAPLLGEIPWLAENPENAATGKYINLALL 224
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220

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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)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

Asymmetric Unit(hide GO term definitions)

Chain A (BIOD1_ECOLI | P13000)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004141	dethiobiotin synthase activity	Catalysis of the reaction: 7,8-diaminononanoate + ATP + CO(2) = ADP + dethiobiotin + 4 H(+) + phosphate.
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
	GO:0009102	biotin biosynthetic process	The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
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.

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