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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM CAMPYLOBACTER JEJUNI

Authors :   Y. Kim, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Str Genomics Of Infectious Diseases (Csgid)

Date :   13 Mar 10 (Deposition) - 28 Apr 10 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Tim Barrel, Csgid, Amino-Acid Biosynthesis, Diaminopimelate Biosynthesis, Lyase, Lysine Biosynthesis, Schiff Base, Structural Genomics, Center For Structural Genomics Of Infectious Diseases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, M. Zhou, K. Kwon, W. F. Anderson, A. Joachimiak, Center For Structural Genomics Of Infectious Diseases (Csgid)
Crystal Structure Of Dihydrodipicolinate Synthase From Campylobacter Jejuni
To Be Published
PubMed: search

Molecule 1 - DIHYDRODIPICOLINATE SYNTHASE
	Chains	:	A, B, C, D
	EC Number	:	4.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	511693
	Gene	:	CJ0806, DAPA
	Organism Scientific	:	CAMPYLOBACTER JEJUNI
	Organism Taxid	:	197
	Strain	:	NCTC 11168
	Synonym	:	DHDPS

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 50)

No.	Name	Count	Type	Full Name
1	CL	10	Ligand/Ion	CHLORIDE ION
2	FMT	1	Ligand/Ion	FORMIC ACID
3	MSE	27	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	3	Ligand/Ion	DI(HYDROXYETHYL)ETHER
5	SO4	9	Ligand/Ion	SULFATE ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:84 , TYR A:110 , HOH A:311 , HOH A:1131 , ASN C:84 , TYR C:110 , HOH C:347	BINDING SITE FOR RESIDUE SO4 A 301
02	AC2	SOFTWARE	ARG A:142 , PHE A:248 , SER A:251 , ASN A:252 , HOH A:496 , HOH A:1071 , HOH A:1144 , LYS C:113	BINDING SITE FOR RESIDUE SO4 A 302
03	AC3	SOFTWARE	ASN A:229 , TYR A:230 , LYS A:231 , GLU A:232	BINDING SITE FOR RESIDUE SO4 A 303
04	AC4	SOFTWARE	LYS A:280	BINDING SITE FOR RESIDUE CL A 304
05	AC5	SOFTWARE	THR A:115 , GLN A:116 , HOH A:328 , HOH A:613	BINDING SITE FOR RESIDUE SO4 A 305
06	AC6	SOFTWARE	ARG B:142 , PHE B:248 , SER B:251 , ASN B:252 , HOH B:447 , HOH B:884 , HOH B:1125 , HOH B:1127 , LYS D:113	BINDING SITE FOR RESIDUE SO4 B 302
07	AC7	SOFTWARE	THR B:115 , GLN B:116 , HOH B:1098 , HOH D:333	BINDING SITE FOR RESIDUE CL B 303
08	AC8	SOFTWARE	GLY B:46 , THR B:47 , ALA B:81 , GLY B:82 , LEU B:105 , VAL B:107 , TYR B:137 , LYS B:166 , HOH B:631 , HOH B:1136 , HOH B:1151	BINDING SITE FOR RESIDUE PEG B 305
09	AC9	SOFTWARE	ASN B:242	BINDING SITE FOR RESIDUE CL B 306
10	BC1	SOFTWARE	LYS C:280	BINDING SITE FOR RESIDUE CL C 301
11	BC2	SOFTWARE	HOH A:584 , THR C:115 , GLN C:116 , HOH C:1072 , HOH C:1105	BINDING SITE FOR RESIDUE CL C 302
12	BC3	SOFTWARE	SER C:277	BINDING SITE FOR RESIDUE CL C 303
13	BC4	SOFTWARE	LYS A:113 , ARG C:142 , PHE C:248 , SER C:251 , ASN C:252 , HOH C:365 , HOH C:1152 , HOH C:1154	BINDING SITE FOR RESIDUE SO4 C 304
14	BC5	SOFTWARE	GLY C:46 , THR C:47 , ALA C:81 , GLY C:82 , LEU C:105 , SER C:106 , VAL C:107 , TYR C:137 , LYS C:166 , HOH C:440 , HOH C:1132 , HOH C:1156	BINDING SITE FOR RESIDUE PEG C 305
15	BC6	SOFTWARE	ASN B:84 , TYR B:110 , ASN D:84 , TYR D:110 , HOH D:382	BINDING SITE FOR RESIDUE SO4 D 301
16	BC7	SOFTWARE	ASN D:229 , TYR D:230 , LYS D:231 , GLU D:232 , HOH D:509	BINDING SITE FOR RESIDUE SO4 D 299
17	BC8	SOFTWARE	LYS D:280	BINDING SITE FOR RESIDUE CL D 302
18	BC9	SOFTWARE	ARG D:60	BINDING SITE FOR RESIDUE CL D 303
19	CC1	SOFTWARE	HOH B:453 , THR D:115 , GLN D:116 , HOH D:1084	BINDING SITE FOR RESIDUE CL D 304
20	CC2	SOFTWARE	LYS B:113 , ARG D:142 , PHE D:248 , SER D:251 , ASN D:252 , HOH D:409 , HOH D:615 , HOH D:628	BINDING SITE FOR RESIDUE SO4 D 305
21	CC3	SOFTWARE	GLY D:46 , THR D:47 , GLY D:82 , LEU D:105 , SER D:106 , VAL D:107 , TYR D:137 , LYS D:166 , HOH D:448 , HOH D:522 , HOH D:1157	BINDING SITE FOR RESIDUE PEG D 306

(no "SS Bond" information available for 3M5V)

Asymmetric/Biological Unit

No.	Residues
1	Asn A:252	-	Pro A:253
2	Leu A:273	-	Pro A:274
3	Asn B:252	-	Pro B:253
4	Leu B:273	-	Pro B:274
5	Asn C:252	-	Pro C:253
6	Leu C:273	-	Pro C:274
7	Asn D:252	-	Pro D:253
8	Leu D:273	-	Pro D:274

(no "SAP(SNP)/Variant" information available for 3M5V)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DHDPS_1	PS00665	Dihydrodipicolinate synthase signature 1.	DAPA_CAMJE	41-58	4	A:41-58 B:41-58 C:41-58 D:41-58
2	DHDPS_2	PS00666	Dihydrodipicolinate synthase signature 2.	DAPA_CAMJE	137-168	4	A:137-168 B:137-168 C:137-168 D:137-168

(no "Exon" information available for 3M5V)

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:298
 aligned with DAPA_CAMJE | Q9PPB4 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:298
                                    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       280       290        
           DAPA_CAMJE     1 MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
               SCOP domains d3m5va_ A: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....ee..eehhhhhhhhhhhhhhh...eee......hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: A:137-168         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m5v A   1 mDKNIIIGAmTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRmmLISGEDAINYPILSNGGKGVISVTSNLLPDmISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAmYLAGLIESLEFRLPLCSPSKENFAKIEEVmKKYKIKGF 298
                            |       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       280       290        
                            |       10-MSE                                                                                                                                                                        185-MSE                         217-MSE                                    260-MSE                       290-MSE    
                            1-MSE                                                                                                                                                                                  186-MSE

Chain B from PDB  Type:PROTEIN  Length:300
 aligned with DAPA_CAMJE | Q9PPB4 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:300
                              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       278       288       298
           DAPA_CAMJE     - --MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
               SCOP domains d3m5vb_ B: automated matches                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh...eeeee....ee..eehhhhhhhhhhhhhh....eee......hhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: B:137-168         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m5v B  -1 NAmDKNIIIGAmTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRmmLISGEDAINYPILSNGGKGVISVTSNLLPDmISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAmYLAGLIESLEFRLPLCSPSKENFAKIEEVmKKYKIKGF 298
                              |      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       278       288 |     298
                              1-MSE   10-MSE                                                                                                                                                                        185-MSE                         217-MSE                                    260-MSE                       290-MSE    
                                                                                                                                                                                                                     186-MSE

Chain C from PDB  Type:PROTEIN  Length:296
 aligned with DAPA_CAMJE | Q9PPB4 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:296
                                    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      
           DAPA_CAMJE     3 KNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
               SCOP domains d3m5vc_ C: automated matches                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..eehhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: C:137-168         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m5v C   3 KNIIIGAmTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRmmLISGEDAINYPILSNGGKGVISVTSNLLPDmISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAmYLAGLIESLEFRLPLCSPSKENFAKIEEVmKKYKIKGF 298
                                   |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      
                                  10-MSE                                                                                                                                                                        185-MSE                         217-MSE                                    260-MSE                       290-MSE    
                                                                                                                                                                                                                 186-MSE

Chain D from PDB  Type:PROTEIN  Length:298
 aligned with DAPA_CAMJE | Q9PPB4 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:298
                                    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       280       290        
           DAPA_CAMJE     1 MDKNIIIGAMTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRMMLISGEDAINYPILSNGGKGVISVTSNLLPDMISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAMYLAGLIESLEFRLPLCSPSKENFAKIEEVMKKYKIKGF 298
               SCOP domains d3m5vd_ D: automated matches                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----DHDPS-3m5vD01 D:6-294                                                                                                                                                                                                                                                                            ---- Pfam domains (1)
           Pfam domains (2) -----DHDPS-3m5vD02 D:6-294                                                                                                                                                                                                                                                                            ---- Pfam domains (2)
           Pfam domains (3) -----DHDPS-3m5vD03 D:6-294                                                                                                                                                                                                                                                                            ---- Pfam domains (3)
           Pfam domains (4) -----DHDPS-3m5vD04 D:6-294                                                                                                                                                                                                                                                                            ---- Pfam domains (4)
         Sec.struct. author .......eeeee....ee..eehhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhh...eeeeehhhhhh...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh...............hhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------DHDPS_1           ------------------------------------------------------------------------------DHDPS_2  PDB: D:137-168         ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m5v D   1 mDKNIIIGAmTALITPFKNGKVDEQSYARLIKRQIENGIDAVVPVGTTGESATLTHEEHRTCIEIAVETCKGTKVKVLAGAGSNATHEAVGLAKFAKEHGADGILSVAPYYNKPTQQGLYEHYKAIAQSVDIPVLLYNVPGRTGCEISTDTIIKLFRDCENIYGVKEASGNIDKCVDLLAHEPRmmLISGEDAINYPILSNGGKGVISVTSNLLPDmISALTHFALDENYKEAKKINDELYNINKILFCESNPIPIKTAmYLAGLIESLEFRLPLCSPSKENFAKIEEVmKKYKIKGF 298
                            |       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       280       290        
                            1-MSE   10-MSE                                                                                                                                                                        185-MSE                         217-MSE                                    260-MSE                       290-MSE    
                                                                                                                                                                                                                   186-MSE

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: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Aldolase (457)

Family: automated matches (113)

Protein domain: automated matches (113)

Campylobacter jejuni [TaxId: 197] (1)

1a	d3m5va_	A:
1b	d3m5vb_	B:
1c	d3m5vc_	C:
1d	d3m5vd_	D:

(no "CATH Domain" information available for 3M5V)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: DHDPS (40)

Campylobacter jejuni (1)

1a	DHDPS-3m5vD01	D:6-294
1b	DHDPS-3m5vD02	D:6-294
1c	DHDPS-3m5vD03	D:6-294
1d	DHDPS-3m5vD04	D:6-294

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (DAPA_CAMJE | Q9PPB4)

molecular function
	GO:0008840	4-hydroxy-tetrahydrodipicolinate synthase	Catalysis of the reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O.
	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: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.
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.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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
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		Leu D:273 - Pro D:274	[ RasMol ]

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Access by PDB/NDB ID
	3m5v
		Family and Domain Information	:	ProDom \| SYSTERS
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	DAPA_CAMJE \| Q9PPB4
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	4.2.1.52
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	DAPA_CAMJE \| Q9PPB4
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UniProtKB/Swiss-Prot
	DAPA_CAMJE \| Q9PPB4	:	3ler 4ly8 4m19 4mlj 4mlr 4r53 5f1u 5f1v

3ler	COMPLEXED WITH PYRUVATE RELATED ID: IDP90711 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 50)

Sites (21, 21)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (1, 4)

Gene Ontology (9, 9)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File