1JCY - JenaLib

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Title :   AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH R5P, PEP AND CADMIUM

Authors :   J. Wang, H. S. Duewel, R. W. Woodard, D. L. Gatti

Date :   11 Jun 01 (Deposition) - 16 Jan 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Kdo8Ps, Kdo8P, Kdo, R5P, Pep, Beta/Alpha Barrel, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Wang, H. S. Duewel, R. W. Woodard, D. L. Gatti
Structures Of Aquifex Aeolicus Kdo8P Synthase In Complex With R5P And Pep, And With A Bisubstrate Inhibitor: Role Of Active Site Water In Catalysis.
Biochemistry V. 40 15676 2001
PubMed-ID: 11747443 | Reference-DOI: 10.1021/BI015568E

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
	Chains	:	A, B
	EC Number	:	4.1.2.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PAAKDSA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	KDO8P SYNTHASE, PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE, 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE, KDO-8- PHOSPHATE SYNTHETASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	CD	2	Ligand/Ion	CADMIUM ION
2	PEP	2	Ligand/Ion	PHOSPHOENOLPYRUVATE
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	R5P	1	Ligand/Ion	RIBOSE-5-PHOSPHATE

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	PEP	4	Ligand/Ion	PHOSPHOENOLPYRUVATE
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	R5P	2	Ligand/Ion	RIBOSE-5-PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:1048 , ARG A:1049 , SER A:1050 , ARG A:1154 , HIS A:1185 , GLN A:1188 , SER A:1197 , PEP A:1268 , HOH A:3204 , ARG B:2106	BINDING SITE FOR RESIDUE R5P A 1269
2	AC2	SOFTWARE	CYS A:1011 , HIS A:1185 , GLU A:1222 , ASP A:1233	BINDING SITE FOR RESIDUE CD A 1270
3	AC3	SOFTWARE	CYS B:2011 , LYS B:2046 , HIS B:2185 , GLU B:2222 , ASP B:2233 , PEP B:2268	BINDING SITE FOR RESIDUE CD B 2270
4	AC4	SOFTWARE	ARG A:1106 , ARG B:2049 , SER B:2050 , HOH B:3203	BINDING SITE FOR RESIDUE PO4 B 2269
5	AC5	SOFTWARE	LYS A:1041 , SER A:1043 , LYS A:1046 , ASP A:1081 , GLN A:1099 , PRO A:1101 , ALA A:1102 , LYS A:1124 , ARG A:1154 , HIS A:1185 , PHE A:1220 , R5P A:1269 , HOH A:3017 , HOH A:3021	BINDING SITE FOR RESIDUE PEP A 1268
6	AC6	SOFTWARE	LYS B:2041 , SER B:2043 , LYS B:2046 , GLN B:2099 , PRO B:2101 , ALA B:2102 , LYS B:2124 , ARG B:2154 , PHE B:2220 , CD B:2270 , HOH B:3031 , HOH B:3070 , HOH B:3090 , HOH B:3205	BINDING SITE FOR RESIDUE PEP B 2268

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

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

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

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

(no "Exon" information available for 1JCY)

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:263
 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 d1jcya_ A: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                           SCOP domains
               CATH domains 1jcyA00 A:1002-1264 Aldolase class I                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee................hhhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhh...eeeee.hhh.ee........ee...hhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jcy A 1002 EKFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 1264
                                  1011      1021      1031      1041      1051      1061      1071      1081      1091      1101      1111      1121      1131      1141      1151      1161      1171      1181      1191      1201      1211      1221      1231      1241      1251      1261

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with KDSA_AQUAE | O66496 from UniProtKB/Swiss-Prot  Length:267

    Alignment length:262
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262  
          KDSA_AQUAE      3 KFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPGGLGDKSGGMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI  264
               SCOP domains d1jcyb_ B: 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)                                                                                                                                                                                          SCOP domains
               CATH domains 1jcyB00 B:2003-2264 Aldolase class I                                                                                                                                                                                                                                   CATH domains
           Pfam domains (1) DAHP_synth_1-1jcyB01 B:2003-2259                                                                                                                                                                                                                                 ----- Pfam domains (1)
           Pfam domains (2) DAHP_synth_1-1jcyB02 B:2003-2259                                                                                                                                                                                                                                 ----- Pfam domains (2)
         Sec.struct. author ..eeeee.....hhhhhhhhhhhhhhhhhhh...eeeee.................hhhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhh...eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhh...eeeee.........-------.hhhhhhhhhhhhhhhh..eeeeeee.hhhhh.......ee..hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1jcy B 2003 KFLVIAGPCAIESEELLLKVGEEIKRLSEKFKEVEFVFKSSFDKANRSSIHSFRGHGLEYGVKALRKVKEEFGLKITTDIHESWQAEPVAEVADIIQIPAFLCRQTDLLLAAAKTGRAVNVKKGQFLAPWDTKNVVEKLKFGGAKEIYLTERGTTFGYNNLVVDFRSLPIMKQWAKVIYDATHSVQLPG-------GMREFIFPLIRAAVAVGCDGVFMETHPEPEKALSDASTQLPLSQLEGIIEAILEIREVASKYYETI 2264
                                  2012      2022      2032      2042      2052      2062      2072      2082      2092      2102      2112      2122      2132      2142      2152      2162      2172      2182        |-      2202      2212      2222      2232      2242      2252      2262  
                                                                                                                                                                                                                     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	d1jcya_	A:
1b	d1jcyb_	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. (15)

1a	1jcyA00	A:1002-1264
1b	1jcyB00	B:2003-2264

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: DAHP_synth_1 (46)

Aquifex aeolicus (17)

1a	DAHP_synth_1-1jcyB01	B:2003-2259
1b	DAHP_synth_1-1jcyB02	B:2003-2259

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.

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1fww	AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP, A5P AND CADMIUM
1jcx	AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH API AND CADMIUM

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

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