2J65 - JenaLib

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Title :   STRUCTURE OF LPXC FROM AQUIFEX AEOLICUS IN COMPLEX WITH UDP

Authors :   L. Buetow, A. Dawson, W. N. Hunter

Date :   26 Sep 06 (Deposition) - 08 Nov 06 (Release) - 16 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Hydrolase, Lipid Synthesis, Lipid A Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Buetow, A. Dawson, W. N. Hunter
The Nucleotide-Binding Site Of Aquifex Aeolicus Lpxc.
Acta Crystallogr. , Sect. F V. 62 1082 2006
PubMed-ID: 17077484 | Reference-DOI: 10.1107/S1744309106041893

Molecule 1 - UDP-3-O-[3-HYDROXYMYRISTOYL] N-ACETYLGLUCOSAMINE DEACETYLASE
	Chains	:	A, B
	EC Number	:	3.5.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A-LPXC C181A D272-282
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET21A
	Fragment	:	RESIDUES 1-271
	Mutation	:	YES
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5
	Synonym	:	UDP-3-O-ACYL-N-ACETYLGLUCOSAMINE DEACETYLASE, UDP-3-O-ACYL-GLCNAC DEACETYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	MYR	3	Ligand/Ion	MYRISTIC ACID
3	UDP	2	Ligand/Ion	URIDINE-5'-DIPHOSPHATE
4	ZN	7	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MYR	1	Ligand/Ion	MYRISTIC ACID
3	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MYR	2	Ligand/Ion	MYRISTIC ACID
3	UDP	1	Ligand/Ion	URIDINE-5'-DIPHOSPHATE
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:74 , THR A:179 , HIS A:226 , ASP A:230 , ZN A:302 , HOH A:2238	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	GLU A:73 , HIS A:253 , ZN A:301 , MYR A:401 , HOH A:2238	BINDING SITE FOR RESIDUE ZN A 302
03	AC3	SOFTWARE	HIS A:58 , HIS A:188 , CL A:305 , HOH A:2239	BINDING SITE FOR RESIDUE ZN A 303
04	AC4	SOFTWARE	GLY A:2 , GLU A:120 , HIS B:29 , GLU B:90	BINDING SITE FOR RESIDUE ZN A 304
05	AC5	SOFTWARE	ASN A:57 , HIS A:58 , PHE A:158 , ZN A:303	BINDING SITE FOR RESIDUE CL A 305
06	AC6	SOFTWARE	HIS B:74 , HIS B:226 , ASP B:230 , ZN B:302 , HOH B:2238	BINDING SITE FOR RESIDUE ZN B 301
07	AC7	SOFTWARE	GLU B:73 , HIS B:253 , ZN B:301 , HOH B:2238 , HOH B:2239	BINDING SITE FOR RESIDUE ZN B 302
08	AC8	SOFTWARE	HIS B:58 , HIS B:188 , CL B:304 , HOH B:2240	BINDING SITE FOR RESIDUE ZN B 303
09	AC9	SOFTWARE	ASN B:57 , HIS B:58 , PHE B:158 , HIS B:188 , ZN B:303 , HOH B:2207	BINDING SITE FOR RESIDUE CL B 304
10	BC1	SOFTWARE	HIS A:58 , SER A:59 , GLU A:73 , GLY A:198 , HIS A:253 , ZN A:302 , HOH A:2238 , HOH A:2241	BINDING SITE FOR RESIDUE MYR A 401
11	BC2	SOFTWARE	ARG A:137 , TYR A:151 , GLY A:153 , GLU A:154 , PHE A:155 , LYS A:156 , GLU A:185 , LYS A:227 , ARG A:250 , GLY A:251	BINDING SITE FOR RESIDUE UDP A 402
12	BC3	SOFTWARE	ILE A:186 , TYR A:212 , ILE B:186 , GLY B:195 , HOH B:2241	BINDING SITE FOR RESIDUE MYR B 401
13	BC4	SOFTWARE	ARG B:137 , TYR B:151 , GLY B:153 , GLU B:154 , PHE B:155 , LYS B:156 , GLU B:185 , LYS B:227 , ARG B:250 , HOH B:2242 , HOH B:2243 , HOH B:2244	BINDING SITE FOR RESIDUE UDP B 402
14	BC5	SOFTWARE	SER A:199 , HOH A:2177 , THR B:179 , ILE B:186 , GLY B:198 , SER B:199 , LEU B:200 , HOH B:2245 , HOH B:2246 , HOH B:2247	BINDING SITE FOR RESIDUE MYR B 403

(no "SS Bond" information available for 2J65)

(no "Cis Peptide Bond" information available for 2J65)

(no "SAP(SNP)/Variant" information available for 2J65)

(no "PROSITE Motif" information available for 2J65)

(no "Exon" information available for 2J65)

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:267
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:267
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
           LPXC_AQUAE     2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQK 268
               SCOP domains d2j65a1 A:2-127 automated matches                                                                                             d2j65a2 A:128-268 automated matches                                                                                                           SCOP domains
               CATH domains 2j65A01 A:2-122 lpxc deacetylase, domain 1                                                                               2j65A02 A:123-268 lpxc deacetylase, domain 2                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee......eeeeeeee......eeeee..eeee.hhh.eee.....eeee..eee..hhhhhhhhhhh....eeeeee..........hhhhhhhhhh.eeeeeee...ee....eeeee..eeeeee....eeeeeeee......eeeeeee..hhhhh.....eee..hhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j65 A   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQK 268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:267
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       
           LPXC_AQUAE     2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQK 268
               SCOP domains d2j65b1 B:2-127 automated matches                                                                                             d2j65b2 B:128-268 automated matches                                                                                                           SCOP domains
               CATH domains 2j65B01 B:2-122 lpxc deacetylase, domain 1                                                                               2j65B02 B:123-268 lpxc deacetylase, domain 2                                                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee......eeeeeeee......eeeee..eeee.hhh.eee.....eeee..eee..hhhhhhhhhhhh...eeeeee..........hhhhhhhhhh.eeeeeee...ee....eeeee..eeeeee.....eeeeeee......eeeeeee..hhhhh.....eee..hhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j65 B   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQK 268
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Ribosomal protein S5 domain 2-like (306)

Superfamily: Ribosomal protein S5 domain 2-like (306)

Family: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC (13)

Protein domain: automated matches (3)

Aquifex aeolicus [TaxId: 224324] (1)

1a	d2j65a1	A:2-127
1b	d2j65a2	A:128-268
1c	d2j65b1	B:2-127
1d	d2j65b2	B:128-268

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: lpxc deacetylase, domain 1 (11)

Homologous Superfamily: lpxc deacetylase, domain 2 (11)

Aquifex aeolicus. Organism_taxid: 224324. Strain: vf5. (1)

1a	2j65A02	A:123-268
1b	2j65B02	B:123-268

Topology: Ribosomal Protein S5; domain 2 (189)

Homologous Superfamily: lpxc deacetylase, domain 1 (11)

Aquifex aeolicus. Organism_taxid: 224324. Strain: vf5. (1)

2a	2j65A01	A:2-122
2b	2j65B01	B:2-122

(no "Pfam Domain" information available for 2J65)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LPXC_AQUAE | O67648)

molecular function
	GO:0008759	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity	Catalysis of the removal of an acetyl group from the 2-N position of glucosamine in the lipid A precursor UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine.
	GO:0103117	UDP-3-O-acyl-N-acetylglucosamine deacetylase activity	Catalysis of the reaction: UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-N-acetylglucosamine(2-) + H2O <=> UDP-3-O-[(3R)-3-hydroxytetradecanoyl]-alpha-D-glucosamine(1-) + acetate
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009245	lipid A biosynthetic process	The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.

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	Cis Peptide Bonds
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	2j65
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1p42	CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE(ZINC-INHIBITED FORM)
1xxe	RDC REFINED SOLUTION STRUCTURE OF THE AALPXC /TU-514 COMPLEX
1yh8	CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASECOMPLEXED WITH PALMITATE
1yhc	CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASECOMPLEXED WITH CACODYLATE
2go3	CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITHIMIDAZOLE.
2go4	CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC COMPLEXED WITHTU-514

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (6, 6)

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