3QY0 - JenaLib

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

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

Date :   02 Mar 11 (Deposition) - 30 Mar 11 (Release) - 27 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Dtbs, Dethiobiotin Synthetase, Structural Genomics, 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 (4, 20)

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:10 , ALA A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , GLU A:116 , GLN A:167 , PO4 A:222 , MG A:223 , MG A:224 , HOH A:270 , HOH A:326 , HOH A:338 , HOH A:420	BINDING SITE FOR RESIDUE GDP A 221
02	AC2	SOFTWARE	THR A:9 , LYS A:13 , LYS A:35 , ASP A:50 , GLU A:116 , GLY A:119 , GDP A:221 , MG A:223 , MG A:224 , HOH A:270 , HOH A:413 , HOH A:429 , HOH A:430	BINDING SITE FOR RESIDUE PO4 A 222
03	AC3	SOFTWARE	THR A:9 , GDP A:221 , PO4 A:222 , MG A:224 , HOH A:270 , HOH A:420 , HOH A:429 , HOH A:430	BINDING SITE FOR RESIDUE MG A 223
04	AC4	SOFTWARE	THR A:14 , ASP A:50 , GLU A:116 , GDP A:221 , PO4 A:222 , MG A:223 , HOH A:270	BINDING SITE FOR RESIDUE MG A 224
05	AC5	SOFTWARE	ASN A:130 , LEU A:132 , ASP A:133 , EDO A:239 , HOH A:315	BINDING SITE FOR RESIDUE EDO A 225
06	AC6	SOFTWARE	PHE A:72 , TYR A:73 , ARG A:74 , TYR A:75 , ASP A:89 , HOH A:436	BINDING SITE FOR RESIDUE EDO A 226
07	AC7	SOFTWARE	LYS A:171 , HIS A:184 , ASN A:200 , PRO A:201 , HOH A:262 , HOH A:383	BINDING SITE FOR RESIDUE EDO A 227
08	AC8	SOFTWARE	THR A:39 , SER A:79 , PRO A:81 , GLY A:119 , VAL A:123	BINDING SITE FOR RESIDUE EDO A 228
09	AC9	SOFTWARE	LYS A:139 , ALA A:140 , LYS A:141 , LEU A:168 , ASP A:169 , HOH A:390	BINDING SITE FOR RESIDUE EDO A 229
10	BC1	SOFTWARE	GLY A:178 , THR A:181 , ASN A:195 , ASN A:199 , GLN A:207 , HOH A:244	BINDING SITE FOR RESIDUE EDO A 230
11	BC2	SOFTWARE	ASN A:42 , ASP A:43 , ARG A:74 , HIS A:76	BINDING SITE FOR RESIDUE EDO A 231
12	BC3	SOFTWARE	THR A:7 , ASN A:8 , THR A:9 , GLY A:119 , GLY A:151 , ASN A:154 , ASP A:155 , HOH A:290	BINDING SITE FOR RESIDUE EDO A 232
13	BC4	SOFTWARE	ASN A:25 , GLY A:28 , LEU A:61 , HOH A:428	BINDING SITE FOR RESIDUE EDO A 233
14	BC5	SOFTWARE	GLN A:22 , ASP A:57	BINDING SITE FOR RESIDUE EDO A 234
15	BC6	SOFTWARE	TYR A:73 , ALA A:92 , PRO A:93 , HOH A:398	BINDING SITE FOR RESIDUE EDO A 235
16	BC7	SOFTWARE	HIS A:0 , MET A:1 , LYS A:139 , LYS A:141 , SER A:220	BINDING SITE FOR RESIDUE EDO A 236
17	BC8	SOFTWARE	CYS A:122 , ASN A:130 , LEU A:157 , TYR A:190 , HOH A:315 , HOH A:356	BINDING SITE FOR RESIDUE EDO A 237
18	BC9	SOFTWARE	PHE A:-3 , HIS A:0 , GLU A:87 , GLU A:88 , LEU A:217 , GLY A:219	BINDING SITE FOR RESIDUE EDO A 238
19	CC1	SOFTWARE	LEU A:157 , ASP A:160 , PHE A:161 , LYS A:164 , EDO A:225	BINDING SITE FOR RESIDUE EDO A 239
20	CC2	SOFTWARE	SER A:64 , ASP A:89 , PRO A:90 , ASN A:91 , HOH A:340	BINDING SITE FOR RESIDUE EDO A 240

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)
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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
	(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_26-3qy0A01 A:1-208                                                                                                                                                                                          ------------ Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhh...eeee..ee..........hhhhhhhhhhh......hhhhhh.ee.....hhhhhhhhhh.....hhhhhhhhhhhh.....eeeee.............hhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh....ee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qy0 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

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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)

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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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
3qxc	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED 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

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