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Title :   THE CRYSTAL STRUCTURE OF 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE FROM YERSINIA PESTIS CO92

Authors :   R. Zhang, N. Maltseva, K. Kwon, W. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)

Date :   19 Mar 09 (Deposition) - 12 May 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   2, 3, 4, 5-Tetrahydropyridine-2-Carboxylate N-Succinyltransferase, Acyltransferase, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lysine Biosynthesis, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Zhang, N. Maltseva, K. Kwon, W. Anderson, A. Joachimiak
The Crystal Structure Of 2, 3, 4, 5-Tetrahydropyridine-2-Carboxylate N-Succinyltransferase From Yersinia Pestis Co92
To Be Published
PubMed: search

Molecule 1 - 2,3,4,5-TETRAHYDROPYRIDINE-2,6-DICARBOXYLATE N- SUCCINYLTRANSFERASE
	Chains	:	A, B, C
	EC Number	:	2.3.1.117
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG19C
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	YERSINIA PESTIS
	Organism Taxid	:	632
	Strain	:	CO92
	Synonym	:	TETRAHYDRODIPICOLINATE N-SUCCINYLTRANSFERASE, THP SUCCINYLTRANSFERASE, TETRAHYDROPICOLINATE SUCCINYLASE

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:346 , HOH A:380 , HOH B:293 , HOH C:284 , HOH C:317	BINDING SITE FOR RESIDUE MG A 275

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:107	-	Pro A:108
2	Glu A:169	-	Pro A:170
3	Pro B:107	-	Pro B:108
4	Glu B:169	-	Pro B:170
5	Pro C:107	-	Pro C:108
6	Glu C:169	-	Pro C:170

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

Asymmetric/Biological Unit (1, 3)

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

(no "Exon" information available for 3GOS)

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:270
 aligned with DAPD_YERPE | Q8ZH69 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:276
                              1                                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268      
           DAPD_YERPE     - --MQQLQNVIETAFERRADITPANVDTVTREAITHVIDLLDTGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVMEGAETRYYDKVPMKFAGYDEARFQREGFRVVPPATVRKGAFIARNTVLMPSYVNIGAFVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFVGARSEVVEGVIVEEGSVISMGVFIGQSTRIYDRETGEVHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRSKVGINELLRTID 274
               SCOP domains d3gosa_ A: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3gosA01 A:-1-70                                                         ----------------3gosA02 A:87-256 Hexapeptide repeat proteins                                                                                                                              ------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhh...eeeee..eeeee.........hhhhhhhhh.ee....ee....ee....ee..eee....ee....ee...eee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee.....ee..ee...eeeeeeeee......eeeeeeeeee...------hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gos A  -1 QSMQQLQNVIETAFERRADITPANVDTVTREAITHVIDLLDTGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVMEGAETRYYDKVPMKFAGYDEARFQREGFRVVPPATVRKGAFIARNTVLMPSYVNIGAFVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFVGARSEVVEGVIVEEGSVISMGVFIGQSTRIYDRETGEVHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDA------GINELLRTID 274
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258      |268      
                                                                                                                                                                                                                                                                                             258    265

Chain B from PDB  Type:PROTEIN  Length:276
 aligned with DAPD_YERPE | Q8ZH69 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:276
                              1                                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268      
           DAPD_YERPE     - --MQQLQNVIETAFERRADITPANVDTVTREAITHVIDLLDTGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVMEGAETRYYDKVPMKFAGYDEARFQREGFRVVPPATVRKGAFIARNTVLMPSYVNIGAFVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFVGARSEVVEGVIVEEGSVISMGVFIGQSTRIYDRETGEVHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRSKVGINELLRTID 274
               SCOP domains d3gosb_ B: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3gosB01 B:-1-70                                                         ----------------3gosB02 B:87-256 Hexapeptide repeat proteins                                                                                                                              ------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhh...eeee....eeee...hhhhh.hhhhhhhhh.ee....ee....ee....ee..eee....ee....ee...eee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee.....ee..ee...eeeeeeeee......eeeeeeeeee......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gos B  -1 QSMQQLQNVIETAFERRADITPANVDTVTREAITHVIDLLDTGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVMEGAETRYYDKVPMKFAGYDEARFQREGFRVVPPATVRKGAFIARNTVLMPSYVNIGAFVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFVGARSEVVEGVIVEEGSVISMGVFIGQSTRIYDRETGEVHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRSKVGINELLRTID 274
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268

Chain C from PDB  Type:PROTEIN  Length:276
 aligned with DAPD_YERPE | Q8ZH69 from UniProtKB/Swiss-Prot  Length:274

    Alignment length:276
                              1                                                                                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268      
           DAPD_YERPE     - --MQQLQNVIETAFERRADITPANVDTVTREAITHVIDLLDTGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVMEGAETRYYDKVPMKFAGYDEARFQREGFRVVPPATVRKGAFIARNTVLMPSYVNIGAFVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFVGARSEVVEGVIVEEGSVISMGVFIGQSTRIYDRETGEVHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRSKVGINELLRTID 274
               SCOP domains d3gosc_ C: automated matches                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3gosC01 C:-1-70                                                         ----------------3gosC02 C:87-256 Hexapeptide repeat proteins                                                                                                                              ------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhh...eeeee..eeeee...hhhhh.hhhhhhhhh.ee....ee....ee....ee..eee....ee....ee...eee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee....eee..ee...eeeeeeeee......eeeeeeeeee......hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gos C  -1 QSMQQLQNVIETAFERRADITPANVDTVTREAITHVIDLLDTGALRVAEKIDGQWVTHQWLKKAVLLSFRINDNQVMEGAETRYYDKVPMKFAGYDEARFQREGFRVVPPATVRKGAFIARNTVLMPSYVNIGAFVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPTIIEDNCFVGARSEVVEGVIVEEGSVISMGVFIGQSTRIYDRETGEVHYGRVPAGSVVVSGNLPSKDGSYSLYCAVIVKKVDAKTRSKVGINELLRTID 274
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268

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: All beta proteins (24004)

Fold: Single-stranded left-handed beta-helix (154)

Superfamily: Trimeric LpxA-like enzymes (147)

Family: Tetrahydrodipicolinate-N-succinlytransferase, THDP-succinlytransferase, DapD (9)

Protein domain: automated matches (3)

Yersinia pestis [TaxId: 632] (1)

1a	d3gosa_	A:
1b	d3gosb_	B:
1c	d3gosc_	C:

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (DAPD_YERPE | Q8ZH69)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:169 - Pro A:170	[ RasMol ]
		Glu B:169 - Pro B:170	[ RasMol ]
		Glu C:169 - Pro C:170	[ RasMol ]
		Pro A:107 - Pro A:108	[ RasMol ]
		Pro B:107 - Pro B:108	[ RasMol ]
		Pro C:107 - Pro C:108	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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Exons (0, 0)

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