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Title :   CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE FROM HELICOBACTER PYLORI COMPLEXED WITH L-LYSINE

Authors :   T. Hu, D. Wu, H. Jiang, X. Shen

Date :   28 Jun 07 (Deposition) - 27 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Diaminopimelate Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Hu, D. Wu, H. Jiang, X. Shen
Crystal Structure Of Diaminopimelate Decarboxylase From Helicobacter Pylori Complexed With L-Lysine
To Be Published
PubMed: search

Molecule 1 - DIAMINOPIMELATE DECARBOXYLASE
	Chains	:	A
	EC Number	:	4.1.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21
	Expression System Vector Type	:	PLASMID
	Gene	:	LYSA
	Organism Scientific	:	HELICOBACTER PYLORI
	Strain	:	SS1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	LYS	1	Mod. Amino Acid	LYSINE
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	LYS	2	Mod. Amino Acid	LYSINE
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:44 , ASP A:65 , HIS A:185 , SER A:188 , GLY A:224 , GLY A:225 , GLU A:259 , PRO A:260 , GLY A:261 , ARG A:262 , TYR A:358 , LYS A:407 , HOH A:1004 , HOH A:1011 , HOH A:1015	BINDING SITE FOR RESIDUE PLP A 406
2	AC2	SOFTWARE	ILE A:148 , ARG A:262 , ARG A:298 , TYR A:302 , CYS A:329 , GLU A:330 , TYR A:358 , MET A:362 , TYR A:366	BINDING SITE FOR RESIDUE LYS A 407
3	AC3	SOFTWARE	LEU A:101 , ASN A:104 , ILE A:105 , LEU A:108 , ALA A:130 , ARG A:131	BINDING SITE FOR RESIDUE GOL A 1003

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

Asymmetric Unit

No.	Residues
1	Thr A:13	-	Pro A:14

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ODR_DC_2_1	PS00878	Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.	DCDA_HELPX	43-61	1	A:43-61

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ODR_DC_2_1	PS00878	Orn/DAP/Arg decarboxylases family 2 pyridoxal-P attachment site.	DCDA_HELPX	43-61	2	A:43-61

(no "Exon" information available for 2QGH)

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:395
 aligned with DCDA_HELPX | B4XMC6 from UniProtKB/Swiss-Prot  Length:405

    Alignment length:401
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402 
           DCDA_HELPX     3 NYEELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGLDLTIICEPGRSIVAESGELITQVLYEKKAQNKRFVIVDAGMNDFLRPSLYHAKHAIRVITPSKGREISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNSRPKLLELALEDHKIRVIRKREALEDLWRLEEEGLK 403
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...eeeeehhhhhhhhhhhhhh.....eeeeee.hhh.hhhhhhhhhhh..eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh..eeeeee.........hhhhh..........hhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhhhhhhh.....eee...............hhhhhhhhhhhhh.....eeee..hhhhhh..eeeeeeeeeee.--...eeee.......hhhhhhh....eee....---..eeeeee........eeeeeeee.......eeee......hhhhh.........eeeee..-.eeeee...hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------ODR_DC_2_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qgh A   3 NYEELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARISIRINPNIDAKTHPYISTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGLDLTIICEPGRSIVAESGELITQVLYEKK--NKRFVIVDAGMNDFLRPSLYHAKHAIRVITPS---EISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGAYGSSMASQYNSRPKLLELALED-KIRVIRKREALEDLWRLEEEGLK 407
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       | -|      292       302       312 |   | 322       332       342       352       362       372      |382       392       402|
                                                                                                                                                                                                                                                                                                               280  |                            314 318                                                          379 |                  402|
                                                                                                                                                                                                                                                                                                                  283                                                                                               381                   407

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 "SCOP Domain" information available for 2QGH)

(no "CATH Domain" information available for 2QGH)

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

Asymmetric Unit(hide GO term definitions)

Chain A (DCDA_HELPX | B4XMC6)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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:0008836	diaminopimelate decarboxylase activity	Catalysis of the reaction: meso-2,6-diaminopimelate + H(+) = L-lysine + CO(2).
	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.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
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: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.

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		Thr A:13 - Pro A:14	[ RasMol ]

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Description

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SS Bonds (0, 0)

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