1YH8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS LPXC DEACETYLASE COMPLEXED WITH PALMITATE

Authors :   M. Hernick, H. A. Gennadios, D. A. Whittington, K. M. Rusche, D. W. Christianson, C. A. Fierke

Date :   07 Jan 05 (Deposition) - 15 Feb 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   X-Ray Crystallography; A. Aeolicus, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hernick, H. A. Gennadios, D. A. Whittington, K. M. Rusche, D. W. Christianson, C. A. Fierke
Udp-3-O-((R)-3-Hydroxymyristoyl)-N- Acetylglucosamine Deacetylase Functions Through A General Acid-Base Catalyst Pair Mechanism
J. Biol. Chem. V. 280 16969 2005
PubMed-ID: 15705580 | Reference-DOI: 10.1074/JBC.M413560200
(for further references see the PDB file header)

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
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	LPXC, ENVA
	Mutation	:	YES
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	UDP-3-O-ACYL-GLCNAC DEACETYLASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	CL	3	Ligand/Ion	CHLORIDE ION
2	PAM	2	Ligand/Ion	PALMITOLEIC ACID
3	ZN	5	Ligand/Ion	ZINC ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:79 , HIS A:238 , ASP A:242 , PAM A:801	BINDING SITE FOR RESIDUE ZN A 501
02	AC2	SOFTWARE	HIS A:58 , HIS A:200	BINDING SITE FOR RESIDUE ZN A 503
03	AC3	SOFTWARE	ILE A:27 , HIS A:29 , GLU A:95 , GLY B:2 , GLU B:126	BINDING SITE FOR RESIDUE ZN A 504
04	AC4	SOFTWARE	HIS B:79 , HIS B:238 , ASP B:242 , PAM B:802	BINDING SITE FOR RESIDUE ZN B 505
05	AC5	SOFTWARE	HIS B:58 , HIS B:200 , CL B:603 , HOH B:863	BINDING SITE FOR RESIDUE ZN B 507
06	AC6	SOFTWARE	HIS A:79 , ILE A:103 , SER A:107	BINDING SITE FOR RESIDUE CL A 601
07	AC7	SOFTWARE	GLY B:15 , VAL B:16 , ILE B:103 , LEU B:104	BINDING SITE FOR RESIDUE CL B 602
08	AC8	SOFTWARE	HIS B:58 , HIS B:200 , ZN B:507	BINDING SITE FOR RESIDUE CL B 603
09	AC9	SOFTWARE	ILE A:18 , HIS A:58 , GLU A:78 , HIS A:79 , THR A:191 , GLY A:210 , HIS A:238 , ASP A:242 , HIS A:265 , ZN A:501	BINDING SITE FOR RESIDUE PAM A 801
10	BC1	SOFTWARE	LEU A:212 , ILE B:18 , HIS B:58 , GLU B:78 , HIS B:79 , THR B:191 , SER B:211 , HIS B:238 , ASP B:242 , HIS B:265 , ZN B:505	BINDING SITE FOR RESIDUE PAM B 802

(no "SS Bond" information available for 1YH8)

(no "Cis Peptide Bond" information available for 1YH8)

(no "SAP(SNP)/Variant" information available for 1YH8)

(no "PROSITE Motif" information available for 1YH8)

(no "Exon" information available for 1YH8)

Asymmetric/Biological 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:266
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:266
                                    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 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQ 267
               SCOP domains d1yh8a1 A:2-127 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                       d1yh8a2 A:128-279 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                                SCOP domains
               CATH domains 1yh8A01 A:2-128 lpxc deacetylase, domain 1                                                                               1yh8A02 A:129-279 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....eeeehhhhhhhhhh..........eeee..............hhhhhhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yh8 A   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQ 279
                                    11        21        31        41        51        61 ||     76        86        96       106       116 ||    127       137       147       157     ||170    || 183       193       203       213       223       233       243       253       263       273      
                                                                                        63|                                              118|                                        163|     175|                                                                                                    
                                                                                         69                                               120                                         167      179

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with LPXC_AQUAE | O67648 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:266
                                    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 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFCFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQ 267
               SCOP domains d1yh8b1 B:2-127 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                       d1yh8b2 B:128-279 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC                                                                SCOP domains
               CATH domains 1yh8B01 B:2-128 lpxc deacetylase, domain 1                                                                               1yh8B02 B:129-279 lpxc deacetylase, domain 2                                                                                                      CATH domains
           Pfam domains (1) LpxC-1yh8B01 B:2-279                                                                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) LpxC-1yh8B02 B:2-279                                                                                                                                                                                                                                                       Pfam domains (2)
         Sec.struct. author .eeeee...eeeeee......eeeeeeee......eeeee..eeee.hhh.eee.....eeee..eee..hhhhhhhhhhhh...eeeeee..........hhhhhhhhhh.eeeeeee...ee....eeeee..eeeeee.....eeeeeee......eeeeeee..hhhhh.....eeehhhhhhhhhh...........eee..............hhhhhhhhhhhhhhhhhhh..ee.eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yh8 B   2 GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHEFVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDGSGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTYEGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLKNTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRGGHSLNVKLVKELAKKQ 279
                                    11        21        31        41        51        61 ||     76        86        96       106       116 ||    127       137       147       157     ||170    || 183       193       203       213       223       233       243       253       263       273      
                                                                                        63|                                              118|                                        163|     175|                                                                                                    
                                                                                         69                                               120                                         167      179

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase LpxC (10)

Aquifex aeolicus [TaxId: 63363] (10)

1a	d1yh8a1	A:2-127
1b	d1yh8a2	A:128-279
1c	d1yh8b1	B:2-127
1d	d1yh8b2	B:128-279

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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: 63363. (10)

1a	1yh8A02	A:129-279
1b	1yh8B02	B:129-279

Topology: Ribosomal Protein S5; domain 2 (189)

Homologous Superfamily: lpxc deacetylase, domain 1 (11)

Aquifex aeolicus. Organism_taxid: 63363. (10)

2a	1yh8A01	A:2-128
2b	1yh8B01	B:2-128

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: S5 (103)

Family: LpxC (10)

Aquifex aeolicus (8)

1a	LpxC-1yh8B01	B:2-279
1b	LpxC-1yh8B02	B:2-279

Asymmetric/Biological 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.

Asymmetric/Biological Unit
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1p42	THE ZINC-INHIBITED ENZYME
1xxe	THE NMR STRUCTURE OF THE ENZYME COMPLEXED WITH TU-514
1yhc

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 4)

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