1KGT - JenaLib

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Title :   CRYSTAL STRUCTURE OF TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE IN COMPLEX WITH PIMELATE AND SUCCINYL-COA

Authors :   T. W. Beaman, K. W. Vogel, D. G. Drueckhammer, J. S. Blanchard, S. L. Rode

Date :   28 Nov 01 (Deposition) - 03 Apr 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Left-Handed Parallel Beta Helix, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. W. Beaman, K. W. Vogel, D. G. Drueckhammer, J. S. Blanchard, S. L. Roderick
Acyl Group Specificity At The Active Site Of Tetrahydridipicolinate N-Succinyltransferase.
Protein Sci. V. 11 974 2002
PubMed-ID: 11910040 | Reference-DOI: 10.1110/PS.4310102

Molecule 1 - 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N- SUCCINYLTRANSFERASE
	Chains	:	A
	EC Number	:	2.3.1.117
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DAPD
	Organism Scientific	:	MYCOBACTERIUM BOVIS
	Organism Taxid	:	1765
	Synonym	:	TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE, THP SUCCINYLTRANSFERASE, TETRAHYDROPICOLINATE SUCCINYLASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (3x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	PML	1	Ligand/Ion	PIMELIC ACID
2	SCA	1	Ligand/Ion	SUCCINYL-COENZYME A

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	PML	3	Ligand/Ion	PIMELIC ACID
2	SCA	3	Ligand/Ion	SUCCINYL-COENZYME A

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:67 , ARG A:104 , ARG A:112 , ASN A:129 , MET A:139 , SER A:148 , GLY A:166 , VAL A:167 , LEU A:168 , GLU A:169 , LEU A:270 , SCA A:302 , HOH A:322	BINDING SITE FOR RESIDUE PML A 301
2	AC2	SOFTWARE	ASP A:141 , THR A:145 , SER A:159 , GLY A:163 , ILE A:164 , GLY A:165 , GLU A:169 , GLY A:185 , ALA A:186 , ARG A:187 , GLU A:189 , VAL A:191 , GLU A:192 , SER A:203 , MET A:204 , SER A:211 , ARG A:213 , ARG A:217 , LYS A:254 , LYS A:259 , THR A:260 , LYS A:263 , PML A:301 , HOH A:323 , HOH A:355	BINDING SITE FOR RESIDUE SCA A 302

(no "SS Bond" information available for 1KGT)

Asymmetric Unit

No.	Residues
1	Pro A:107	-	Pro A:108
2	Glu A:169	-	Pro A:170

(no "SAP(SNP)/Variant" information available for 1KGT)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEXAPEP_TRANSFERASES	PS00101	Hexapeptide-repeat containing-transferases signature.	DAPD_UNKP	134-162	1	A:134-162

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HEXAPEP_TRANSFERASES	PS00101	Hexapeptide-repeat containing-transferases signature.	DAPD_UNKP	134-162	3	A:134-162

(no "Exon" information available for 1KGT)

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
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Chain A from PDB  Type:PROTEIN  Length:274
 aligned with DAPD_UNKP | P56220 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:274
                                    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    
            DAPD_UNKP     1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
               SCOP domains d1kgta_ A: Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD                                                                                                                                                                                            SCOP domains
               CATH domains 1kgtA01 A:1-70                                                        ----------------1kgtA02 A:87-256 Hexapeptide repeat proteins                                                                                                                              ------------------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhhh..eeee....eeee.........hhhhhhhhh.ee....ee....ee....ee...ee....ee....ee....ee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee.....ee..ee...eeeeeeeee......eeeeeeeeee.hhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kgt A   1 MQQLQNVIESAFERRADITPANVDTVTREAVNQVIGLLDSGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNKVMDGAETRYYDKVPMKFADYDEARFQKEGFRVVPPATVRQGAFIARNTVLMPSYVNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFIGARSEVVEGVIVEEGSVISMGVYLGQSTRIYDRETGEIHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRGKVGINELLRTID 274
                                    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

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 '\|'

(no "Pfam Domain" information available for 1KGT)

Asymmetric Unit(hide GO term definitions)

Chain A (DAPD_UNKP | P56220)

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.

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	Cis Peptide Bonds
		Glu A:169 - Pro A:170	[ RasMol ]
		Pro A:107 - Pro A:108	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	1kgt
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	DAPD_UNKP \| P56220
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	2.3.1.117
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	DAPD_UNKP \| P56220
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UniProtKB/Swiss-Prot
	DAPD_UNKP \| P56220	:	1kgq 1tdt 2tdt 3tdt

1kgq	CRYSTAL STRUCTURE OF TETRAHYDRODIPICOLINATE N- SUCCINYLTRANSFERASE IN COMPLEX WITH L-2-AMINOPIMELATE AND SUCCINAMIDE-COA
1tdt	1TDT CONTAINS THE APOENZYME STRUCTURE OF DAPD
2tdt	2TDT CONTAINS DAPD IN COMPLEX WITH L-2-AMINOPIMELATE AND COENZYME A
3tdt	3TDT CONTAINS DAPD IN COMPLEX WITH L-2-AMINO-6-OXOPIMELATE AND COENZYME A

Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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SCOP Domains (1, 1)

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Gene Ontology (8, 8)

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