3EG4 - JenaLib

Title :   CRYSTAL STRUCTURE OF 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE FROM BRUCELLA MELITENSIS BIOVAR ABORTUS 2308

Authors :   Seattle Structural Genomics Center For Infectious Disease (Ssgcid)

Date :   10 Sep 08 (Deposition) - 23 Sep 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.87

Chains :   Asym. Unit : A
Biol. Unit 1: A  (3x)
Biol. Unit 2: A  (1x)

Keywords :   Ssgcid, Transferase, N-Succinyl-Transferase, Beta Helix, Acyltransferase, Amino-Acid Biosynthesis, Cytoplasm, Diaminopimelate Biosynthesis, Lysine Biosynthesis, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Ssgcid
Crystal Structure Of 2, 3, 4, 5-Tetrahydropyridine-2-Carboxylate N-Succinyltransferase From Brucella Melitensis Biovar Abortus 2308
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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:279
 aligned with DAPD_BRUSU | Q8FV25 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:279
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275         
           DAPD_BRUSU     6 LASLEKTIEKAFDERDGINTATRGEVREAVEQSLILLDRGEVRVAEKQADGNWHVNQWLKKAVLLSFRLNPMEVIKGGPGQSSWWDKVPSKFDGWTANEFEKAGFRAVPNCIVRHSAYIAPNAILMPSFVNLGAYVDKGAMIDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRATGEVFYGEVPPYSVVVAGTMPGKNVPGENWGPSLYCAVIVKRADEKTRSKTSINELLRD 284
               SCOP domains d3eg4a_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 3eg4A01 A:6-75                                                        ------------------3eg4A02 A:94-269 Hexapeptide repeat proteins                                                                                                                                    --------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....eee.....eeehhhhhhhhhhhhhhh..eeee.hhhh.eeee.........hhhhhhhhh.ee....ee....ee....ee..eee....ee....ee...eee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee.....ee..ee...eeeeeeeee...........eeeeeeeeee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eg4 A   6 LASLEKTIEKAFDERDGINTATRGEVREAVEQSLILLDRGEVRVAEKQADGNWHVNQWLKKAVLLSFRLNPMEVIKGGPGQSSWWDKVPSKFDGWTANEFEKAGFRAVPNCIVRHSAYIAPNAILMPSFVNLGAYVDKGAMIDTWATVGSCAQIGKNVHLSGGVGIGGVLEPMQAGPTIIEDNCFIGARSEVVEGCIVREGSVLGMGVFIGKSTKIVDRATGEVFYGEVPPYSVVVAGTMPGKNVPGENWGPSLYCAVIVKRADEKTRSKTSINELLRD 284
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (DAPD_BRUSU | Q8FV25)

molecular function
	GO:0008666	2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity	Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H(2)O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA.
	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.
	GO:0016746	transferase activity, transferring acyl groups	Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3eg4)

	Sites
(no "Sites" information available for 3eg4)

	Cis Peptide Bonds
		Glu A:176 - Pro A:177	[ RasMol ]
		Pro A:114 - Asn A:115	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3eg4
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	DAPD_BRUSU \| Q8FV25
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.3.1.117
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description