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

Authors :   M. Chruszcz, X. Xu, M. Cuff, M. Cymborowski, H. Zheng, A. Savchenko, A. E A. Joachimiak, W. Minor, Midwest Center For Structural Genomics

Date :   16 Jul 07 (Deposition) - 31 Jul 07 (Release) - 27 Mar 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.47

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

Keywords :   Dethiobiotin Synthetase, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Atp-Binding, Biotin Biosynthesis, Ligase, Magnesium, Nucleotide- Binding (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

Molecule 1 - DETHIOBIOTIN SYNTHETASE
	Atcc	:	700392
	Chains	:	A
	EC Number	:	6.3.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P11
	Expression System Strain	:	BL21-GOLD (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BIOD, HP_0029
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	85962
	Strain	:	26695
	Synonym	:	DETHIOBIOTIN SYNTHASE, DTB SYNTHETASE, DTBS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:151 , LEU A:152 , ILE A:153 , SER A:187	BINDING SITE FOR RESIDUE CL A 301
2	AC2	SOFTWARE	LYS A:13 , THR A:14 , HOH A:517	BINDING SITE FOR RESIDUE CL A 302

(no "SS Bond" information available for 2QMO)

Asymmetric Unit

No.	Residues
1	Gly A:-1	-	His A:0

(no "SAP(SNP)/Variant" information available for 2QMO)

(no "PROSITE Motif" information available for 2QMO)

(no "Exon" information available for 2QMO)

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:220
 aligned with BIOD_HELPY | O24872 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:220
                              1                                                                                                                                                                                                                         
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218
           BIOD_HELPY     - --MLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENMLDFALKLKAKMLLISHDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLMSFALK 218
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2qmoA00 A:-1-218 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                        CATH domains
               Pfam domains --AAA_26-2qmoA01 A:1-208                                                                                                                                                                                          ---------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeee..ee..........hhhhhhhhhhh......hhhhhh.ee.....hhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeee.............hhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhh....ee...hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qmo A  -1 GHmLFISATNTNAGKTTCARLLAQYCNACGVKTILLKPIETGVNDAINHSSDAHLFLQDNRLLDRSLTLKDISFYRYHKVSAPLIAQQEEDPNAPIDTDNLTQRLHNFTKTYDLVIVEGAGGLCVPITLEENmLDFALKLKAKmLLISHDNLGLINDCLLNDFLLKSHQLDYKIAINLKGNNTAFHSISLPYIELFNTRSNNPIVIFQQSLKVLmSFALK 218
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128  |    138   |   148       158       168       178       188       198       208    |  218
                              |                                                                                                                               131-MSE    142-MSE                                                                213-MSE 
                              1-MSE

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 2QMO)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Helicobacter pylori 26695. Organism_taxid: 85962. Strain: 26695. (8)

2qmoA00

A:-1-218

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: AAA_26 (9)

Helicobacter pylori (Campylobacter pylori) (8)

AAA_26-2qmoA01

A:1-208

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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	Cis Peptide Bonds
		Gly A:-1 - His A:0	[ RasMol ]

Biological Unit
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	2qmo
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	BIOD_HELPY \| O24872
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	BIOD_HELPY \| O24872	:	3mle 3qxc 3qxh 3qxj 3qxs 3qxx 3qy0

(no "Related Entries Specified in the PDB File" available for 2QMO)

Description

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Ligands, Modified Residues, Ions (2, 6)

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SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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