3QXX - JenaLib

Title :   CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH GDP AND 8-AMINOCAPRYLIC ACID

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 :   1.36

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 (6, 12)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:9 , THR A:39 , SER A:79 , VAL A:123 , GLY A:151 , LEU A:152 , ILE A:153 , ASN A:154 , PO4 A:225 , HOH A:252 , HOH A:291 , HOH A:293 , HOH A:377	BINDING SITE FOR RESIDUE 8AC A 221
02	AC2	SOFTWARE	ASN A:10 , ALA A:11 , GLY A:12 , LYS A:13 , THR A:14 , THR A:15 , GLU A:116 , ASN A:175 , LYS A:177 , GLY A:178 , MG A:223 , MG A:224 , PO4 A:225 , HOH A:261 , HOH A:269 , HOH A:290 , HOH A:303 , HOH A:413 , HOH A:517 , HOH A:534	BINDING SITE FOR RESIDUE GDP A 222
03	AC3	SOFTWARE	GDP A:222 , MG A:224 , PO4 A:225 , HOH A:269 , HOH A:289 , HOH A:290 , HOH A:517	BINDING SITE FOR RESIDUE MG A 223
04	AC4	SOFTWARE	THR A:14 , LYS A:35 , ASP A:50 , GLU A:116 , GDP A:222 , MG A:223 , PO4 A:225 , HOH A:517	BINDING SITE FOR RESIDUE MG A 224
05	AC5	SOFTWARE	THR A:9 , LYS A:13 , LYS A:35 , ASP A:50 , GLU A:116 , ALA A:118 , GLY A:119 , 8AC A:221 , GDP A:222 , MG A:223 , MG A:224 , HOH A:255 , HOH A:289 , HOH A:290 , HOH A:493	BINDING SITE FOR RESIDUE PO4 A 225
06	AC6	SOFTWARE	ASN A:42 , ASP A:43 , ARG A:74 , HIS A:76	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	LYS A:171 , ASN A:200 , PRO A:201 , HOH A:474 , HOH A:511	BINDING SITE FOR RESIDUE EDO A 228
09	AC9	SOFTWARE	PHE A:72 , TYR A:73 , ARG A:74 , TYR A:75 , ASP A:89 , HOH A:314 , HOH A:555	BINDING SITE FOR RESIDUE EDO A 229
10	BC1	SOFTWARE	GLN A:22 , ASP A:57 , HOH A:557	BINDING SITE FOR RESIDUE EDO A 230
11	BC2	SOFTWARE	TYR A:73 , ALA A:92 , PRO A:93	BINDING SITE FOR RESIDUE EDO A 231
12	BC3	SOFTWARE	ASN A:130 , ASP A:133 , HIS A:166 , HOH A:285 , HOH A:397	BINDING SITE FOR RESIDUE GOL A 232

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_26-3qxxA01 A:1-208                                                                                                                                                                                          ------------ Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhhhhhhh...eeee..ee..........hhhhhhhhhhh......hhhhhh.ee.....hhhhhhhhhh.....hhhhhhhhhhhhhhh..eeeee.............hhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh....ee...hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qxx 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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		8AC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qxx)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3qxx
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	BIOD_HELPY \| O24872
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	6.3.3.3
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

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
3qy0	CRYSTAL STRUCTURE OF DETHIOBIOTIN SYNTHETASE (BIOD) FROM HELICOBACTER PYLORI COMPLEXED WITH GDP

Description