3QXC - JenaLib

Title :   CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH ATP

Authors :   P. J. Porebski, M. M. Klimecka, M. Chruszcz, K. Murzyn, A. Joachimiak, W Midwest Center For Structural Genomics (Mcsg)

Date :   01 Mar 11 (Deposition) - 30 Mar 11 (Release) - 27 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.34

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

Keywords :   Dtbs, Dethiobiotin Synthetase, Structural Genomics, Atp Binding, Psi- Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. J. Porebski, M. Klimecka, M. Chruszcz, R. A. Nicholls, K. Murzyn, M. E. Cuff, X. Xu, M. Cymborowski, G. N. Murshudov, A. Savchenko, A. Edwards, W. Minor
Structural Characterization Of Helicobacter Pylori Dethiobiotin Synthetase Reveals Differences Between Family Members.
Febs J. V. 279 1093 2012
PubMed-ID: 22284390 | Reference-DOI: 10.1111/J.1742-4658.2012.08506.X

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 17)

Sites (17, 17)

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:9 , ASN A:10 , ALA A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , LYS A:35 , ASP A:50 , GLU A:116 , GLN A:167 , ASN A:175 , LYS A:177 , MG A:222 , HOH A:278 , HOH A:291 , HOH A:294 , HOH A:358 , HOH A:362 , HOH A:366 , HOH A:412 , HOH A:486 , HOH A:559	BINDING SITE FOR RESIDUE ATP A 221
02	AC2	SOFTWARE	THR A:14 , ASP A:50 , GLU A:116 , ATP A:221 , HOH A:362	BINDING SITE FOR RESIDUE MG A 222
03	AC3	SOFTWARE	SER A:5 , ALA A:6 , LYS A:13 , GLY A:117 , ALA A:118 , GLY A:119 , GLY A:120 , LEU A:121 , MET A:131 , HOH A:284	BINDING SITE FOR RESIDUE NO3 A 223
04	AC4	SOFTWARE	ASN A:130 , LEU A:132 , ASP A:133 , LEU A:162 , HIS A:166 , HOH A:254	BINDING SITE FOR RESIDUE EDO A 224
05	AC5	SOFTWARE	ASN A:42 , ASP A:43 , ARG A:74 , HIS A:76 , HOH A:288 , HOH A:499	BINDING SITE FOR RESIDUE EDO A 225
06	AC6	SOFTWARE	ASN A:25 , GLY A:28 , LYS A:30 , LEU A:61 , HOH A:258 , HOH A:272	BINDING SITE FOR RESIDUE EDO A 226
07	AC7	SOFTWARE	HIS A:0 , MET A:1 , LYS A:139 , LYS A:141 , SER A:220	BINDING SITE FOR RESIDUE EDO A 227
08	AC8	SOFTWARE	GLN A:22 , ASP A:57 , HOH A:536	BINDING SITE FOR RESIDUE EDO A 228
09	AC9	SOFTWARE	ASN A:179 , ASN A:180 , THR A:181 , ALA A:182 , HOH A:247 , HOH A:328 , HOH A:509 , HOH A:558	BINDING SITE FOR RESIDUE EDO A 229
10	BC1	SOFTWARE	ASN A:8 , HIS A:147 , ASN A:149 , HOH A:466	BINDING SITE FOR RESIDUE EDO A 230
11	BC2	SOFTWARE	LEU A:157 , ASP A:160 , PHE A:161 , LYS A:164 , HOH A:254 , HOH A:271	BINDING SITE FOR RESIDUE EDO A 231
12	BC3	SOFTWARE	LEU A:168 , ASP A:169 , TYR A:170 , ASN A:200 , HOH A:270 , HOH A:432	BINDING SITE FOR RESIDUE EDO A 232
13	BC4	SOFTWARE	CYS A:122 , GLU A:129 , ASN A:130 , LEU A:157 , TYR A:190 , HOH A:254 , HOH A:397 , HOH A:435	BINDING SITE FOR RESIDUE GOL A 233
14	BC5	SOFTWARE	ASN A:199 , ILE A:202 , HOH A:255 , HOH A:551	BINDING SITE FOR RESIDUE EDO A 234
15	BC6	SOFTWARE	THR A:9 , THR A:39 , GLY A:40 , VAL A:78 , SER A:79 , HOH A:294	BINDING SITE FOR RESIDUE EDO A 235
16	BC7	SOFTWARE	LYS A:171 , HIS A:184 , ASN A:199 , ASN A:200 , PRO A:201 , VAL A:211 , HOH A:310 , HOH A:398	BINDING SITE FOR RESIDUE PEG A 236
17	BC8	SOFTWARE	PHE A:72 , TYR A:73 , ARG A:74 , TYR A:75 , ASP A:89 , HOH A:282	BINDING SITE FOR RESIDUE EDO A 237

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

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:224
 aligned with BIOD_HELPY | O24872 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:224
                                1                                                                                                                                                                                                                      218  
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216 |  
           BIOD_HELPY     - ----MLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLMSFALK--   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----AAA_26-3qxcA01 A:1-208                                                                                                                                                                                          ------------ Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhh...eeee..ee..........hhhhhhhhhhhh.....hhhhhh.ee.....hhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeee.............hhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh....ee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxc A  -3 FQGHMLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLMSFALKGS 220
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (BIOD_HELPY | O24872)

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.

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	3qxc
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

2qmo	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI
3mle	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COCRYSTALLIZED WITH ATP
3qxh	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH ADP AND 8-AMINOCAPRYLIC ACID
3qxj	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH GTP
3qxs	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH ANP
3qxx	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH GDP AND 8-AMINOCAPRYLIC ACID
3qy0	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH GDP

Description