3C5Q - JenaLib

Title :   CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE (I148L MUTANT) FROM HELICOBACTER PYLORI COMPLEXED WITH L-LYSINE

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

Date :   01 Feb 08 (Deposition) - 27 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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, J. Ding, H. Jiang, X. Shen
Crystal Structure Of Diaminopimelate Decarboxylase From Helicobacter Pylori
To Be Published
PubMed: search

Compounds

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
	Mutation	:	YES
	Organism Scientific	:	HELICOBACTER PYLORI
	Strain	:	SS1

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 3)

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

Sites (3, 3)

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: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 , HOH A:1120	BINDING SITE FOR RESIDUE PLP A 406
2	AC2	SOFTWARE	LEU A:148 , ARG A:262 , ARG A:298 , TYR A:302 , 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 , ARG A:131	BINDING SITE FOR RESIDUE GOL A 1003

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

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

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: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...eeeeehhhhhhhhhhhhhhh....eeeeee.hhh.hhhhhhhhhhh..eeee.hhhhhhhhhhhh.hhh.eee.....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh..eeeeee.........hhhhh..........hhhhhhhhhhhhhhh..eeeeeee.........hhhhhhhhhhhhhhhhhhhhh.....eee...............hhhhhhhhhhhhh.....eeee..hhhhhh..eeeeeeeeeee.--...eeee.......hhhhhhh....eee....---.eeeeeee........eeeeeeeee......eeee......hhhhh.........eeeee..-.eeeee...hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------ODR_DC_2_1         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c5q A   3 NYEELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLSILSLLAHLESGADCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALKLNILFLNVESFMELKTIETIAQSLGIKARISIRINPNIDAKTHPYLSTGLKENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLDLEPIIEASQKVAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGLDLTIICEPGRSIVAESGELITQVLYEKK--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)
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	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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

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