2VC6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   STRUCTURE OF MOSA FROM S. MELILOTI WITH PYRUVATE BOUND

Authors :   C. P. Phenix, K. H. Nienaber, P. H. Tam, L. T. J. Delbaere, D. R. J. Palmer

Date :   18 Sep 07 (Deposition) - 17 Jun 08 (Release) - 09 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Dhdps, Tim Barrel, Schiff Base, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. P. Phenix, K. H. Nienaber, P. H. Tam, L. T. J. Delbaere, D. R. J. Palmer
Structural, Functional And Calorimetric Investigation Of Mosa, A Dihydrodipicolinate Synthase From Sinorhizobium Meliloti L5-30, Does Not Support Involvement In Rhizopine Biosynthesis.
Chembiochem V. 9 1591 2008
PubMed-ID: 18536061 | Reference-DOI: 10.1002/CBIC.200700569

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
	Chains	:	A, B
	EC Number	:	4.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC18
	Expression System Strain	:	AT997
	Expression System Taxid	:	562
	Organism Scientific	:	SINORHIZOBIUM MELILOTI
	Organism Taxid	:	382
	Other Details	:	PYRUVATE COVALENTLY BOUND TO K161
	Strain	:	L5-30
	Synonym	:	MOSA

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	MCL	2	Mod. Amino Acid	NZ-(1-CARBOXYETHYL)-LYSINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MCL	4	Mod. Amino Acid	NZ-(1-CARBOXYETHYL)-LYSINE

(no "Site" information available for 2VC6)

(no "SS Bond" information available for 2VC6)

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 2VC6)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_1	PS00665	Dihydrodipicolinate synthase signature 1.	DAPA_RHIML	37-54	2	A:37-54 B:37-54
2	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	DAPA_RHIML	132-163	2	A:132-163 B:132-163

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_RHIML	37-54	4	A:37-54 B:37-54
2	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	DAPA_RHIML	132-163	4	A:132-163 B:132-163

(no "Exon" information available for 2VC6)

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_RHIML | Q07607 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_RHIML     1 MFEGSITALVTPFADDRIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVEITIKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKAIDAASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVKDATGNLLRPSLERMACGEDFNLLTGEDGTALGYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDRLMPLHRALFLETNPAGAKYALQRLGRMRGDLRLPLVTISPSFQEEIDDAMRHAGILL 292
               SCOP domains d2vc6a_ A: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2vc6A00 A:1-292 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeee.hhhhhh...hhhhhhhhhhhh..eeee......hhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: A:132-163         --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vc6 A   1 MFEGSITALVTPFADDRIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVEITIKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKAIDAASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVkDATGNLLRPSLERMACGEDFNLLTGEDGTALGYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDRLMPLHRALFLETNPAGAKYALQRLGRMRGDLRLPLVTISPSFQEEIDDAMRHAGILL 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-MCL

Chain B from PDB  Type:PROTEIN  Length:292
 aligned with DAPA_RHIML | Q07607 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_RHIML     1 MFEGSITALVTPFADDRIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVEITIKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKAIDAASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVKDATGNLLRPSLERMACGEDFNLLTGEDGTALGYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDRLMPLHRALFLETNPAGAKYALQRLGRMRGDLRLPLVTISPSFQEEIDDAMRHAGILL 292
               SCOP domains d2vc6b_ B: automated matches                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2vc6B00 B:1-292 Aldolase class I                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....ee..eehhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhh....eeee.hhhhhh...hhhhhhhhhhhh..eeee......hhhhhhhhhhh....eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..............hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------DHDPS_1           -----------------------------------------------------------------------------DHDPS_2  PDB: B:132-163         --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vc6 B   1 MFEGSITALVTPFADDRIDEVALHDLVEWQIEEGSFGLVPCGTTGESPTLSKSEHEQVVEITIKTANGRVPVIAGAGSNSTAEAIAFVRHAQNAGADGVLIVSPYYNKPTQEGIYQHFKAIDAASTIPIIVYNIPGRSAIEIHVETLARIFEDCPNVKGVkDATGNLLRPSLERMACGEDFNLLTGEDGTALGYMAHGGHGCISVTANVAPALCADFQQACLNGDFAAALKLQDRLMPLHRALFLETNPAGAKYALQRLGRMRGDLRLPLVTISPSFQEEIDDAMRHAGILL 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-MCL

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Rhizobium meliloti (Sinorhizobium meliloti) [TaxId: 382] (1)

1a	d2vc6a_	A:
1b	d2vc6b_	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)

Sinorhizobium meliloti. Organism_taxid: 382. Strain: l5-30. (1)

1a	2vc6A00	A:1-292
1b	2vc6B00	B:1-292

(no "Pfam Domain" information available for 2VC6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (DAPA_RHIML | Q07607)

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.

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	Cis Peptide Bonds
		Asn A:248 - Pro A:249	[ RasMol ]
		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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Cis Peptide Bonds (4, 4)

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