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Title :   CRYSTAL STRUCTURE OF DIAMINOPIMELATE DECARBOXYLASE FROM M. JANNASCHI

Authors :   K. Rajashankar, S. R. Ray, J. B. Bonanno, M. G. Pinho, G. He, H. De Lencastre, A. Tomasz, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)

Date :   24 Jun 04 (Deposition) - 20 Jul 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Antibiotic Resistance, Diamnopimilate Decarboxylase, Lysine Biosynthesis, Structural Genomics, Nysgxrc, T135, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Rajashankar, S. R. Ray, J. B. Bonanno, M. G. Pinho, G. He, H. De Lencastre, A. Tomasz, S. K. Burley
Cocrystal Structures Of Diaminopimelate Decarboxylase: Mechanism, Evolution, And Inhibition Of An Antibiotic Resistance Accessory Factor
Structure V. 10 1499 2002
PubMed-ID: 12429091 | Reference-DOI: 10.1016/S0969-2126(02)00880-8
(for further references see the PDB file header)

Molecule 1 - DIAMINOPIMELATE DECARBOXYLASE
	Chains	:	A, B
	EC Number	:	4.1.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET T7
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	LYSA, MJ1097
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Synonym	:	DAP DECARBOXYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	AZ1	2	Ligand/Ion	AZELAIC ACID
2	LLP	2	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	AZ1	2	Ligand/Ion	AZELAIC ACID
2	LLP	2	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	AZ1	4	Ligand/Ion	AZELAIC ACID
2	LLP	4	Mod. Amino Acid	2-LYSINE(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHANE)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LLP A:83 , HIS A:224 , GLY A:226 , SER A:227 , ARG A:307 , ARG A:343 , TYR A:347 , HOH A:532 , GLU B:373 , SER B:374 , TYR B:409	BINDING SITE FOR RESIDUE AZ1 A 502
2	AC2	SOFTWARE	CYS A:372 , GLU A:373 , SER B:227 , ARG B:307 , ARG B:343 , TYR B:347	BINDING SITE FOR RESIDUE AZ1 B 503

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

Asymmetric Unit

No.	Residues
1	Thr A:44	-	Pro A:45
2	Thr B:44	-	Pro B:45

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

Asymmetric Unit (2, 4)

	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_METJA	70-88	2	A:80-98 B:80-98
2	ODR_DC_2_2	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.	DCDA_METJA	243-256	2	A:253-266 B:253-266

Biological Unit 1 (2, 4)

	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_METJA	70-88	2	A:80-98 B:80-98
2	ODR_DC_2_2	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.	DCDA_METJA	243-256	2	A:253-266 B:253-266

Biological Unit 2 (2, 8)

	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_METJA	70-88	4	A:80-98 B:80-98
2	ODR_DC_2_2	PS00879	Orn/DAP/Arg decarboxylases family 2 signature 2.	DCDA_METJA	243-256	4	A:253-266 B:253-266

(no "Exon" information available for 1TUF)

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:434
 aligned with DCDA_METJA | Q58497 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:434
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434    
           DCDA_METJA     5 FLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELGETANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDLADAIINTMLKYKDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINCKVKNEKEVVSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAKDIVPPHLL 438
               SCOP domains d1tufa1 A:15-49,A:314-448          d1tufa2 A:50-313 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                                     d1tufa1 A:15-49,A:314-448 Diaminopimelate decarboxylase LysA                                                                            SCOP domains
               CATH domains 1tufA01 A:15-50,A:307-448           1tufA02 A:51-306 Alanine racemase                                                                                                                                                                                                                               1tufA01 A:15-50,A:307-448 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee....eee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhh.hhhhhhhhhhh..eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh..eeeee.ee.......hhhhhhhhhhh...ee...hhhhhhhhhhhh...eee.eee........hhhhhhhhhhhhhhhhhhhhh......eee................hhhhhhhhhhhhhhh........eeee..hhhhhh..eeeeeeeeeeee....eeeee.......hhhhhhh....eee......eeeeeee........eeeeeeeee......eeee......hhhhh.........eeeeee..eeeeee...hhhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------ODR_DC_2_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tuf A  15 FLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYkANANLAITRLLAKLGCGADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELGETANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDLADAIINTMLKYKDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINCKVKNEKEVVSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAKDIVPPHLL 448
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444    
                                                                                               83-LLP

Chain B from PDB  Type:PROTEIN  Length:434
 aligned with DCDA_METJA | Q58497 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:434
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434    
           DCDA_METJA     5 FLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYKANANLAITRLLAKLGCGADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELGETANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDLADAIINTMLKYKDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINCKVKNEKEVVSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAKDIVPPHLL 438
               SCOP domains d1tufb1 B:15-49,B:314-448          d1tufb2 B:50-313 Diaminopimelate decarboxylase LysA                                                                                                                                                                                                                     d1tufb1 B:15-49,B:314-448 Diaminopimelate decarboxylase LysA                                                                            SCOP domains
               CATH domains 1tufB01 B:15-50,B:307-448           1tufB02 B:51-306 Alanine racemase                                                                                                                                                                                                                               1tufB01 B:15-50,B:307-448 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                    CATH domains
           Pfam domains (1) -------------------------------------------Orn_Arg_deC_N-1tufB01 B:58-312                                                                                                                                                                                                                                 ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------Orn_Arg_deC_N-1tufB02 B:58-312                                                                                                                                                                                                                                 ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Orn_DAP_Arg_deC-1tufB03 B:236-420                                                                                                                                                        ---------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Orn_DAP_Arg_deC-1tufB04 B:236-420                                                                                                                                                        ---------------------------- Pfam domains (4)
         Sec.struct. author ......eee....eee..eehhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhh.hhhhhhhhhhh..eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhh...eeee.hhhhhhhhhhhhhhhh..eeeeeeee.......hhhhhhhhhhh...ee...hhhhhhhhhhh....eeeeeee.........hhhhhhhhhhhhhhhhhhhh......eee................hhhhhhhhhhhhhhh........eeee..hhhhhh..eeeeeeeeeeee....eeeee.......hhhhhhh....eee......eeeeeee........eeeeeeeee......eeee......hhhhh.........eeeeee..eeeeee...hhhhhh.....hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------ODR_DC_2_1         ----------------------------------------------------------------------------------------------------------------------------------------------------------ODR_DC_2_2    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tuf B  15 FLGNDTVEIKDGRFFIDGYDAIELAEKFGTPLYVMSEEQIKINYNRYIEAFKRWEEETGKEFIVAYAYkANANLAITRLLAKLGCGADVVSGGELYIAKLSNVPSKKIVFNGNCKTKEEIIMGIEANIRAFNVDSISELILINETAKELGETANVAFRINPNVNPKTHPKISTGLKKNKFGLDVESGIAMKAIKMALEMEYVNVVGVHCHIGSQLTDISPFIEETRKVMDFVVELKEEGIEIEDVNLGGGLGIPYYKDKQIPTQKDLADAIINTMLKYKDKVEMPNLILEPGRSLVATAGYLLGKVHHIKETPVTKWVMIDAGMNDMMRPAMYEAYHHIINCKVKNEKEVVSIAGGLCESSDVFGRDRELDKVEVGDVLAIFDVGAYGISMANNYNARGRPRMVLTSKKGVFLIRERETYADLIAKDIVPPHLL 448
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444    
                                                                                               83-LLP

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 Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Alanine racemase (53)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (2)

1a	1tufA02	A:51-306
1b	1tufB02	B:51-306

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Homologous Superfamily: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (2)

2a	1tufA01	A:15-50,A:307-448
2b	1tufB01	B:15-50,B:307-448

Asymmetric Unit(hide GO term definitions)

Chain A,B (DCDA_METJA | Q58497)

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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