3DEN - JenaLib

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Title :   STRUCTURE OF E. COLI DHDPS MUTANT Y107W

Authors :   F. G. Pearce, J. A. Gerrard, M. A. Perugini, G. B. Jameson

Date :   10 Jun 08 (Deposition) - 25 Nov 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Dihydrodipicolinate Synthase, Monomer, Quaternary Structure, Amino- Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. G. Pearce, R. C. J. Dobson, A. Weber, L. A. Lane, M. G. Mccammon, M. A. Squire, M. A. Perugini, G. B. Jameson, C. V. Robinson, J. A. Gerrar
Mutating The Tight-Dimer Interface Of Dihydrodipicolinate Synthase Disrupts The Enzyme Quaternary Structure: Toward A Monomeric Enzyme
Biochemistry V. 47 12108 2008
PubMed-ID: 18937497 | Reference-DOI: 10.1021/BI801094T

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
	Chains	:	A, B
	EC Number	:	4.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PJG001
	Expression System Strain	:	XL1-BLUE
	Expression System Taxid	:	562
	Expression System Vector Type	:	PBLUESCRIPT
	Gene	:	DAPA
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Synonym	:	DHDPS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	K	2	Ligand/Ion	POTASSIUM ION
3	KGC	2	Mod. Amino Acid	N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE
4	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 16)

No.	Name	Count	Type	Full Name
1	GOL	6	Ligand/Ion	GLYCEROL
2	K	-1	Ligand/Ion	POTASSIUM ION
3	KGC	4	Mod. Amino Acid	N~6~-[(2R)-2-CARBOXY-5-OXOTETRAHYDROFURAN-2-YL]-L-LYSINE
4	PO4	6	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:152 , VAL A:154 , LYS A:155 , ILE A:157 , HOH A:501	BINDING SITE FOR RESIDUE K A 293
2	AC2	SOFTWARE	ASP A:29 , ALA A:33 , HIS A:125 , GOL A:295	BINDING SITE FOR RESIDUE GOL A 294
3	AC3	SOFTWARE	LYS A:26 , TYR A:30 , HIS A:125 , GOL A:294	BINDING SITE FOR RESIDUE GOL A 295
4	AC4	SOFTWARE	ARG A:109	BINDING SITE FOR RESIDUE PO4 A 296
5	AC5	SOFTWARE	ALA A:81 , GLU A:84 , HOH A:312 , HOH A:439 , HOH A:440 , ALA B:49 , THR B:50 , LEU B:51 , ASN B:52	BINDING SITE FOR RESIDUE GOL A2647
6	AC6	SOFTWARE	ALA B:152 , VAL B:154 , LYS B:155 , ILE B:157	BINDING SITE FOR RESIDUE K B 293
7	AC7	SOFTWARE	HOH A:523 , ARG B:21 , LYS B:25 , HOH B:356	BINDING SITE FOR RESIDUE PO4 B 294
8	AC8	SOFTWARE	TYR B:116 , LYS B:120 , ARG B:150 , HOH B:432 , HOH B:449	BINDING SITE FOR RESIDUE PO4 B 295

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

Asymmetric Unit

No.	Residues
1	Asn A:248	-	Pro A:249
2	Leu A:269	-	Pro A:270
3	Asn B:248	-	Pro B:249
4	Leu B:269	-	Pro B:270

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

Asymmetric Unit (2, 4)

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

Biological Unit 1 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_1	PS00665	Dihydrodipicolinate synthase signature 1.	DAPA_ECOLI	38-55	4	A:38-55 B:38-55
2	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	DAPA_ECOLI	133-163	4	A:133-163 B:133-163

(no "Exon" information available for 3DEN)

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:292
 aligned with DAPA_ECOLI | P0A6L2 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_ECOLI     1 MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL 292
               SCOP domains d3dena_ A: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3denA00 A:1-292 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh.......eeeee.......hhhhhhhhhhhhhhh....eeee.hhhhhh...hhhhhhhhhh...eeee.......hhhhhhhh......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: A:133-163        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3den A   1 MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYWNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIkEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL 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  
                                                                                                                                                                                          161-KGC

Chain B from PDB  Type:PROTEIN  Length:292
 aligned with DAPA_ECOLI | P0A6L2 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_ECOLI     1 MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL 292
               SCOP domains d3denb_ B: Dihydrodipicolinate synthase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3denB00 B:1-292 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...........hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh.......eeeee.......hhhhhhhhhhhhhhh....eeee.hhhhhh...hhhhhhhhh....eeee.......hhhhhhhh......eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: B:133-163        --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3den B   1 MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYWNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIkEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL 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  
                                                                                                                                                                                          161-KGC

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 aldolase (182)

Protein domain: Dihydrodipicolinate synthase (30)

Escherichia coli K-12 [TaxId: 83333] (3)

1a	d3dena_	A:
1b	d3denb_	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)

Escherichia coli k-12. Organism_taxid: 83333. (2)

1a	3denA00	A:1-292
1b	3denB00	B:1-292

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (DAPA_ECOLI | P0A6L2)

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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:248 - Pro A:249	[ RasMol ]
		Asn B:248 - Pro B:249	[ RasMol ]
		Leu A:269 - Pro A:270	[ RasMol ]
		Leu B:269 - Pro B:270	[ RasMol ]

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	3den
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(no "Related Entries Specified in the PDB File" available for 3DEN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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