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Title :   CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM PSEUDOMONAS AERUGINOSA

Authors :   N. Kaur, S. Kumar, N. Singh, A. Gautam, R. Sharma, S. Sharma, R. Tewari, T

Date :   25 Jun 10 (Deposition) - 28 Jul 10 (Release) - 28 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

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

Keywords :   Lys Biosynthesis Pathway, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Kaur, S. Kumar, N. Singh, A. Gautam, R. Sharma, S. Sharma, R. Tewari, T. P. Singh
Crystal Structure Of Dihydrodipicolinate Synthase From Pseudomonas Aeruginosa
To Be Published
PubMed: search

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
	Chains	:	A, B
	EC Number	:	4.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28C(+)
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208964
	Strain	:	PAO1
	Synonym	:	DAP-A

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 8)

No.	Name	Count	Type	Full Name
1	PGO	8	Ligand/Ion	S-1,2-PROPANEDIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:268 , HOH A:360	BINDING SITE FOR RESIDUE PGO A 293
2	AC2	SOFTWARE	GLN A:112	BINDING SITE FOR RESIDUE PGO A 294
3	AC3	SOFTWARE	HOH A:362	BINDING SITE FOR RESIDUE PGO A 295
4	AC4	SOFTWARE	GLY A:69 , ARG A:70 , HOH A:371 , HOH A:372 , GLN B:283 , GLN B:287	BINDING SITE FOR RESIDUE PGO A 296
5	AC5	SOFTWARE	HOH B:365	BINDING SITE FOR RESIDUE PGO B 293
6	AC6	SOFTWARE	MET B:1 , ASP B:98	BINDING SITE FOR RESIDUE PGO B 294
7	AC7	SOFTWARE	LYS B:109 , PRO B:110 , GLN B:112 , CYS B:141 , ASP B:142	BINDING SITE FOR RESIDUE PGO B 295
8	AC8	SOFTWARE	LYS A:93 , LEU B:197	BINDING SITE FOR RESIDUE PGO B 296

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

Asymmetric/Biological Unit

No.	Residues
1	Leu A:268	-	Pro A:269
2	Asn B:248	-	Pro B:249
3	Leu B:268	-	Pro B:269

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_1	PS00665	Dihydrodipicolinate synthase signature 1.	DAPA_PSEAE	38-55	2	A:38-55 B:38-55
2	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	DAPA_PSEAE	133-163	2	A:133-163 B:133-163

(no "Exon" information available for 3NOE)

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:292
 aligned with DAPA_PSEAE | Q9I4W3 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:292
                                    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       290  
           DAPA_PSEAE     1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIRRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRHIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDFLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHKALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVLA 292
               SCOP domains d3noea_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee...hhhhhhhhhhhh....eeee....hhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: A:133-163        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3noe A   1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQDGTNAIVAVGTTGESATLDVEEHIQVVRRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRHIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDFLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHKALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPHCHDPLRQAMRQTGVLA 292
                                    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       290

Chain B from PDB  Type:PROTEIN  Length:292
 aligned with DAPA_PSEAE | Q9I4W3 from UniProtKB/Swiss-Prot  Length:292

    Alignment length:292
                                    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       290  
           DAPA_PSEAE     1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVIRRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRHIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDFLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHKALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVLA 292
               SCOP domains d3noeb_ B: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhh...eeeeee.....hhhhhhhhhh....eeee....hhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: B:133-163        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3noe B   1 MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQDGTNAIVAVGTTGESATLDVEEHIQVVRRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQHFRHIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERVGKDFLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLMPLHKALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPHCHDPLRQAMRQTGVLA 292
                                    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       290

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 aldolase (182)

Protein domain: automated matches (54)

Pseudomonas aeruginosa [TaxId: 208964] (1)

1a	d3noea_	A:
1b	d3noeb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (DAPA_PSEAE | Q9I4W3)

molecular function
	GO:0008840	4-hydroxy-tetrahydrodipicolinate synthase	Catalysis of the reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O.
	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:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0019877	diaminopimelate biosynthetic process	The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
	GO:0009085	lysine biosynthetic process	The chemical reactions and pathways resulting in the formation of lysine, 2,6-diaminohexanoic acid.
	GO:0009089	lysine biosynthetic process via diaminopimelate	The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
	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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	Cis Peptide Bonds
		Asn B:248 - Pro B:249	[ RasMol ]
		Leu A:268 - Pro A:269	[ RasMol ]
		Leu B:268 - Pro B:269	[ RasMol ]

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	3noe
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	DAPA_PSEAE \| Q9I4W3	:	3ps7 3puo 3qze 3s8h

1yxc	STRUCTURE OF E. COLI DIHYDRODIPICOLINATE SYNTHASE TO 1.9 A
3flu	CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM THE PATHOGEN NEISSERIA MENINGITIDIS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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