3STG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A58P, DEL(N59), AND LOOP 7 TRUNCATED MUTANT OF 3-DEOXY-D-MANNO-OCTULOSONATE 8-PHOSPHATE SYNTHASE (KDO8PS) FROM NEISSERIA MENINGITIDIS

Authors :   T. M. Allison, G. B. Jameson, E. J. Parker

Date :   09 Jul 11 (Deposition) - 23 Nov 11 (Release) - 23 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Manno-Octulosonate, Synthase, Lipopolysaccharide, Kdop, Kdo8 Kdops, Kdo8Ps, Tim Barrel, Biosynthesis, Transferase, Lyase, Lipopolysaccharide Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. M. Allison, R. D. Hutton, W. Jiao, B. J. Gloyne, E. B. Nimmo, G. B. Jameson, E. J. Parker
An Extended (Beta)7(Alpha)7 Substrate-Binding Loop Is Essential For Efficient Catalysis By 3-Deoxy-D-Manno-Octulosonate 8-Phosphate Synthase
Biochemistry V. 50 9318 2011
PubMed-ID: 21942786 | Reference-DOI: 10.1021/BI201231E

Molecule 1 - 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
	Chains	:	A, B, C, D
	EC Number	:	2.5.1.55
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PT7-7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	KDSA, NMB1283
	Mutation	:	YES
	Organism Scientific	:	NEISSERIA MENINGITIDIS
	Organism Taxid	:	122586
	Strain	:	MC58
	Synonym	:	3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHASE, KDO- 8-PHOSPHATE SYNTHASE, KDO 8-P SYNTHASE, KDOPS, PHOSPHO-2-DEHYDRO-3- DEOXYOCTONATE ALDOLASE

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 12)

No.	Name	Count	Type	Full Name
1	CL	12	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ALA A:112 , GLN A:137	BINDING SITE FOR RESIDUE CL A 269
02	AC2	SOFTWARE	GLN A:109 , LYS A:134 , HIS A:198 , PHE A:222	BINDING SITE FOR RESIDUE CL A 270
03	AC3	SOFTWARE	LYS A:57 , PRO A:58 , ARG A:59 , HOH A:349	BINDING SITE FOR RESIDUE CL A 271
04	AC4	SOFTWARE	GLY B:201 , ARG B:202 , HOH B:343	BINDING SITE FOR RESIDUE CL B 269
05	AC5	SOFTWARE	GLN B:109 , LYS B:134 , HIS B:198 , PHE B:222 , HOH B:600	BINDING SITE FOR RESIDUE CL B 270
06	AC6	SOFTWARE	LYS B:57 , PRO B:58 , ARG B:59	BINDING SITE FOR RESIDUE CL B 271
07	AC7	SOFTWARE	ALA B:112 , GLN B:137	BINDING SITE FOR RESIDUE CL B 272
08	AC8	SOFTWARE	ALA C:112 , GLN C:137	BINDING SITE FOR RESIDUE CL C 269
09	AC9	SOFTWARE	LYS C:57 , PRO C:58 , ARG C:59	BINDING SITE FOR RESIDUE CL C 270
10	BC1	SOFTWARE	ALA D:112 , PHE D:113 , GLN D:137 , ARG D:164	BINDING SITE FOR RESIDUE CL D 269
11	BC2	SOFTWARE	GLN D:109 , LYS D:134 , HIS D:198 , PHE D:222	BINDING SITE FOR RESIDUE CL D 270
12	BC3	SOFTWARE	LYS D:57 , PRO D:58 , ARG D:59	BINDING SITE FOR RESIDUE CL D 271

(no "SS Bond" information available for 3STG)

(no "Cis Peptide Bond" information available for 3STG)

(no "SAP(SNP)/Variant" information available for 3STG)

(no "PROSITE Motif" information available for 3STG)

(no "Exon" information available for 3STG)

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
	(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:260
 aligned with KDSA_NEIMB | Q9JZ55 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:280
                                    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       270       280
           KDSA_NEIMB     1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPILTIE 280
               SCOP domains d3stga_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee....-..........hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee..hhhhhhhhhhh....eeee.....-----------.hhhhhhhhhhhhhh....eeeeeee..--------...ee..hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3stg A   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKP-RSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSL-----------GRRAQALDLALAGMATRLAGLFLESHPD--------PSALPLHLLEDFLIRIKALDDLIKSQPILTIE 268
                                    10        20        30        40        50       |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199|        -  |    208       218       228       238       248       258       268
                                                                                    58 |                                                                                                                                          200         201                        228      237                               
                                                                                      59

Chain B from PDB  Type:PROTEIN  Length:268
 aligned with KDSA_NEIMB | Q9JZ55 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:280
                                    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       270       280
           KDSA_NEIMB     1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPILTIE 280
               SCOP domains d3stgb_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee....-.........hhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee.hhhhhhhhhhhh....eeee.hhhh-----------....hhhhhhhhhhh....eeeee................hhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3stg B   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKP-RSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSL-----------GRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPILTIE 268
                                    10        20        30        40        50       |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199|        -  |    208       218       228       238       248       258       268
                                                                                    58 |                                                                                                                                          200         201                                                                   
                                                                                      59

Chain C from PDB  Type:PROTEIN  Length:260
 aligned with KDSA_NEIMB | Q9JZ55 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:280
                                    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       270       280
           KDSA_NEIMB     1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPILTIE 280
               SCOP domains d3stgc_ C: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee....-..........hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeee..ee.....ee...hhhhhhhhhh....eeee.....-----------.hhhhhhhhhhhhhh....eeeee....--------....hhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3stg C   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKP-RSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSL-----------GRRAQALDLALAGMATRLAGLFLESHPD--------PSALPLHLLEDFLIRIKALDDLIKSQPILTIE 268
                                    10        20        30        40        50       |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199|        -  |    208       218       228       238       248       258       268
                                                                                    58 |                                                                                                                                          200         201                        228      237                               
                                                                                      59

Chain D from PDB  Type:PROTEIN  Length:258
 aligned with KDSA_NEIMB | Q9JZ55 from UniProtKB/Swiss-Prot  Length:280

    Alignment length:280
                                    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       270       280
           KDSA_NEIMB     1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKANRSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSLQTRDAGSAASGGRRAQALDLALAGMATRLAGLFLESHPDPKLAKCDGPSALPLHLLEDFLIRIKALDDLIKSQPILTIE 280
               SCOP domains d3stgd_ D: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eee......eeeeeeee..hhhhhhhhhhhhhhhhhhhh..eeeeee....-..........hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh.eeeehhhhh.hhhhhhhhhhhh.eeeee........hhhhhhhhhhhh....eeeee..ee.....ee.hhhhhhhhhhhh....eeee.hhhh-----------.hhhhhhhhhhhhhh....eeeeeee.----------..ee..hhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3stg D   1 MDIKINDITLGNNSPFVLFGGINVLESLDSTLQTCAHYVEVTRKLGIPYIFKASFDKP-RSSIHSYRGVGLEEGLKIFEKVKAEFGIPVITDVHEPHQCQPVAEVCDVIQLPAFLARQTDLVVAMAKTGNVVNIKKPQFLSPSQMKNIVEKFHEAGNGKLILCERGSSFGYDNLVVDMLGFGVMKQTCGNLPVIFDVTHSL-----------GRRAQALDLALAGMATRLAGLFLESHP----------SALPLHLLEDFLIRIKALDDLIKSQPILTIE 268
                                    10        20        30        40        50       |59        69        79        89        99       109       119       129       139       149       159       169       179       189       199|        -  |    208       218        |-       238       248       258       268
                                                                                    58 |                                                                                                                                          200         201                       227        238                              
                                                                                      59

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) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: Class I DAHP synthetase (87)

Protein domain: automated matches (27)

Neisseria meningitidis [TaxId: 122586] (16)

1a	d3stga_	A:
1b	d3stgb_	B:
1c	d3stgc_	C:
1d	d3stgd_	D:

(no "CATH Domain" information available for 3STG)

(no "Pfam Domain" information available for 3STG)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (KDSA_NEIMB | Q9JZ55)

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/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (8, 8)

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