1PE1 - JenaLib

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Title :   AQUIFEX AEOLICUS KDO8PS IN COMPLEX WITH CADMIUM AND 2-PGA

Authors :   J. Wang, X. Xu, C. Grison, S. Petek, P. Coutrot, M. R. Birck, R. W. Woodard D. L. Gatti

Date :   20 May 03 (Deposition) - 03 Feb 04 (Release) - 16 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.74

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

Keywords :   Beta(8)/Alpha(8) Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Xu, J. Wang, C. Grison, S. Petek, P. Coutrot, M. R. Birck, R. W. Woodard, D. L. Gatti
Structure-Based Design Of Novel Inhibitors Of 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase
Drug Des. Discovery V. 18 91 2003
PubMed-ID: 14675946

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
	Chains	:	A, B
	EC Number	:	4.1.2.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PAAKDSA
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	KDSA
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE, 3-DEOXY-D-MANNO- OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE, KDO-8-PHOSPHATE SYNTHETASE, KDO 8-P SYNTHASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	2PG	2	Ligand/Ion	2-PHOSPHOGLYCERIC ACID
2	CD	2	Ligand/Ion	CADMIUM ION
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	2PG	4	Ligand/Ion	2-PHOSPHOGLYCERIC ACID
2	CD	-1	Ligand/Ion	CADMIUM ION
3	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:1049 , SER A:1050 , HOH A:3098 , HOH A:3141 , HOH A:3398 , ARG B:2106	BINDING SITE FOR RESIDUE PO4 A 1269
2	AC2	SOFTWARE	ARG A:1106 , ARG B:2049 , SER B:2050 , HOH B:3030 , HOH B:3112 , HOH B:3235	BINDING SITE FOR RESIDUE PO4 B 2269
3	AC3	SOFTWARE	CYS A:1011 , HIS A:1185 , GLU A:1222 , ASP A:1233 , HOH A:3231	BINDING SITE FOR RESIDUE CD A 1270
4	AC4	SOFTWARE	CYS B:2011 , HIS B:2185 , GLU B:2222 , ASP B:2233 , HOH B:3252	BINDING SITE FOR RESIDUE CD B 2270
5	AC5	SOFTWARE	LYS A:1041 , SER A:1043 , LYS A:1046 , ASN A:1048 , ASP A:1081 , GLN A:1099 , PRO A:1101 , ALA A:1102 , LYS A:1124 , ARG A:1154 , HIS A:1185 , PHE A:1220 , GLU A:1222 , HOH A:3017 , HOH A:3058 , HOH A:3150 , HOH A:3236	BINDING SITE FOR RESIDUE 2PG A 1268
6	AC6	SOFTWARE	LYS B:2041 , SER B:2043 , LYS B:2046 , ASP B:2081 , GLN B:2099 , PRO B:2101 , ALA B:2102 , LYS B:2124 , ARG B:2154 , HIS B:2185 , PHE B:2220 , HOH B:3025 , HOH B:3074 , HOH B:3144	BINDING SITE FOR RESIDUE 2PG B 2268

(no "SS Bond" information available for 1PE1)

(no "Cis Peptide Bond" information available for 1PE1)

(no "SAP(SNP)/Variant" information available for 1PE1)

(no "PROSITE Motif" information available for 1PE1)

(no "Exon" information available for 1PE1)

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:258
 aligned with KDSA_AQUAE | O66496 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:264
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260    
          KDSA_AQUAE      1 MEKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI  264
               SCOP domains d1pe1a_ A: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                            SCOP domains
               CATH domains 1pe1A00 A:1001-1264 Aldolase class I                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.................hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhh...eeeee.hhhhh...------..hhhhhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1pe1 A 1001 MEKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPG------GGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 1264
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190|     1200      1210      1220      1230      1240      1250      1260    
                                                                                                                                                                                                                       1191   1198

Chain B from PDB  Type:PROTEIN  Length:256
 aligned with KDSA_AQUAE | O66496 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:263
                                    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   
          KDSA_AQUAE      2 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI  264
               SCOP domains d1pe1b_ B: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                           SCOP domains
               CATH domains 1pe1B00 B:2002-2264 Aldolase class I                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) DAHP_synth_1-1pe1B01 B:2002-2259                                                                                                                                                                                                                                  ----- Pfam domains (1)
           Pfam domains (2) DAHP_synth_1-1pe1B02 B:2002-2259                                                                                                                                                                                                                                  ----- Pfam domains (2)
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhh...eeeee.hhhhh...-------.hhhhhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pe1 B 2002 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPG-------GMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 2264
                                  2011      2021      2031      2041      2051      2061      2071      2081      2091      2101      2111      2121      2131      2141      2151      2161      2171      2181      2191      2201      2211      2221      2231      2241      2251      2261   
                                                                                                                                                                                                                      2191    2199

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: Class I DAHP synthetase (87)

Protein domain: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase) (44)

Aquifex aeolicus [TaxId: 63363] (32)

1a	d1pe1a_	A:
1b	d1pe1b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Aquifex aeolicus. Organism_taxid: 63363. (20)

1a	1pe1A00	A:1001-1264
1b	1pe1B00	B:2002-2264

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: DAHP_synth_1 (46)

Aquifex aeolicus (17)

1a	DAHP_synth_1-1pe1B01	B:2002-2259
1b	DAHP_synth_1-1pe1B02	B:2002-2259

Asymmetric Unit(hide GO term definitions)

Chain A,B (KDSA_AQUAE | O66496)

molecular function
	GO:0008676	3-deoxy-8-phosphooctulonate synthase activity	Catalysis of the reaction: D-arabinose 5-phosphate + H(2)O + phosphoenolpyruvate = 8-phospho-3-deoxy-D-manno-oct-2-ulosonate + 2 H(+) + phosphate.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0009058	biosynthetic process	The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
	GO:0019294	keto-3-deoxy-D-manno-octulosonic acid biosynthetic process	The chemical reactions and pathways resulting in the formation of keto-3-deoxy-D-manno-octulosonic acid, an acidic sugar present in lipopolysaccharides of the outer membranes of some Gram-negative bacteria.
	GO:0009103	lipopolysaccharide biosynthetic process	The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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1fws	AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP AND CADMIUM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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SCOP Domains (1, 2)

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