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(-) Description

Title :  CRYSTAL STRUCTURE OF 2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE FROM ENTEROCOCCUS FAECALIS V583
 
Authors :  K. Tan, L. Bigelow, S. Clancy, A. Joachimiak, Midwest Center For Str Genomics (Mcsg)
Date :  12 Mar 08  (Deposition) - 25 Mar 08  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Apc86892, 2, 3, 4, 5-Tetrahydropyridine-2-Carboxylate N- Succinyltransferase, Enterococcus Faecalis V583, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, L. Bigelow, S. Clancy, A. Joachimiak
The Crystal Structure Of 2, 3, 4, 5-Tetrahydropyridine-2-Carboxylate N-Succinyltransferase From Enterococcus Faecalis V583.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2,3,4,5-TETRAHYDROPYRIDINE-2,6-DICARBOXYLATE N- ACETYLTRANSFERASE
    Atcc: 700802
    Chains: A, B, C
    EC Number: 2.3.1.89
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: DAPD, DAPH, EF_1133
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351
    Strain: V583
    Synonym: TETRAHYDRODIPICOLINATE N-ACETYLTRANSFERASE, THP ACETYLTRANSFERASE, TETRAHYDROPICOLINATE ACETYLASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 31)

Asymmetric/Biological Unit (6, 31)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL6Ligand/IonCHLORIDE ION
3FMT7Ligand/IonFORMIC ACID
4MG1Ligand/IonMAGNESIUM ION
5MSE15Mod. Amino AcidSELENOMETHIONINE
6PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC2SOFTWAREASN B:116 , GLY B:135 , GLY B:153BINDING SITE FOR RESIDUE CL B 302
02AC3SOFTWAREASN C:116 , GLY C:134 , GLY C:135 , GLY C:153BINDING SITE FOR RESIDUE CL C 303
03AC4SOFTWAREASN A:116 , GLY A:135 , GLY A:153BINDING SITE FOR RESIDUE CL A 304
04AC5SOFTWAREARG B:98 , ARG C:90BINDING SITE FOR RESIDUE CL B 305
05AC6SOFTWAREARG A:90 , ARG C:98BINDING SITE FOR RESIDUE CL C 306
06AC7SOFTWAREARG A:98 , ARG B:90BINDING SITE FOR RESIDUE CL A 307
07AC8SOFTWAREGLY A:192 , GLY B:192 , GLY C:192BINDING SITE FOR RESIDUE ACT A 316
08AC9SOFTWARELEU A:82 , GLU A:102 , ILE A:103BINDING SITE FOR RESIDUE FMT A 308
09BC1SOFTWARELEU A:178 , ALA B:190 , ALA B:191BINDING SITE FOR RESIDUE FMT B 309
10BC2SOFTWARELEU C:82 , ILE C:87 , ILE C:103BINDING SITE FOR RESIDUE FMT C 310
11BC3SOFTWAREALA A:191 , ALA A:206BINDING SITE FOR RESIDUE FMT A 311
12BC4SOFTWAREGLU B:71 , ASN B:72BINDING SITE FOR RESIDUE FMT B 312
13BC5SOFTWAREALA C:190 , ALA C:191 , ALA C:193 , ALA C:206 , GLY C:207BINDING SITE FOR RESIDUE PEG C 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CJ8)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Glu A:156 -Pro A:157
2Val A:208 -Pro A:209
3Glu B:156 -Pro B:157
4Val B:208 -Pro B:209
5Glu C:156 -Pro C:157
6Val C:208 -Pro C:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CJ8)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HEXAPEP_TRANSFERASESPS00101 Hexapeptide-repeat containing-transferases signature.DAPH_ENTFA171-199
 
 		  3A:171-199
B:171-199
C:171-199

(-) Exons   (0, 0)

(no "Exon" information available for 3CJ8)

(-) Sequences/Alignments

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:219
 aligned with DAPH_ENTFA | Q836H8 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:219
                             1                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209         
           DAPH_ENTFA     - -MDAYEIIQYIGDAKKQTLVKVTLKGQLKEVTFPETIKVFNNCKTGTLFGDWADVKPFLEANKEKIEDYVVENDARNSAIPFLDLKDINARIEPGALIREKVEIGDQAVIMMGAILNIGAVVGAGTMIDMGAVLGGRATVGKHCHIGAGTVLAGVIEPPSAAPVVIENEVVIGANAVVLEGVRVGEGAVVAAGAVVVEDVPAHTVVAGVPAKVIKQIDD 218
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cj8A01 A:0-133cj8A02 A:14-78  [code=3.30.70.250, no name defined]             3cj8A03 A:79-218 Hexapeptide repeat proteins                                                                                                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh....eeeeeeee...........eeee...eeeeeeehhhhhhhhhhh...eeeeeeee.................ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee............ee....ee....ee....ee....ee....ee.......eeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cj8 A   0 AmDAYEIIQYIGDAKKQTLVKVTLKGQLKEVTFPETIKVFNNCKTGTLFGDWADVKPFLEANKEKIEDYVVENDARNSAIPFLDLKDINARIEPGALIREKVEIGDQAVImmGAILNIGAVVGAGTmIDmGAVLGGRATVGKHCHIGAGTVLAGVIEPPSAAPVVIENEVVIGANAVVLEGVRVGEGAVVAAGAVVVEDVPAHTVVAGVPAKVIKQIDD 218
                             |       9        19        29        39        49        59        69        79        89        99       109||     119      |129       139       149       159       169       179       189       199       209         
                             |                                                                                                          110-MSE         126-MSE                                                                                        
                             1-MSE                                                                                                       111-MSE           129-MSE                                                                                     


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with DAPH_ENTFA | Q836H8 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:218
                              1                                                                                                                                                                                                                       
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        
           DAPH_ENTFA     - --MDAYEIIQYIGDAKKQTLVKVTLKGQLKEVTFPETIKVFNNCKTGTLFGDWADVKPFLEANKEKIEDYVVENDARNSAIPFLDLKDINARIEPGALIREKVEIGDQAVIMMGAILNIGAVVGAGTMIDMGAVLGGRATVGKHCHIGAGTVLAGVIEPPSAAPVVIENEVVIGANAVVLEGVRVGEGAVVAAGAVVVEDVPAHTVVAGVPAKVIKQI 216
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cj8B01 B:-1-133cj8B02 B:14-79  [code=3.30.70.250, no name defined]              3cj8B03 B:80-216 Hexapeptide repeat proteins                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....eeeeeeee.hhhh......eeee...eeeeeeehhhhhhhhhhh...eeeeeeee.................ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee............ee....ee....ee....ee....ee....ee.......eeee....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ----------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cj8 B  -1 NAmDAYEIIQYIGDAKKQTLVKVTLKGQLKEVTFPETIKVFNNCKTGTLFGDWADVKPFLEANKEKIEDYVVENDARNSAIPFLDLKDINARIEPGALIREKVEIGDQAVImmGAILNIGAVVGAGTmIDmGAVLGGRATVGKHCHIGAGTVLAGVIEPPSAAPVVIENEVVIGANAVVLEGVRVGEGAVVAAGAVVVEDVPAHTVVAGVPAKVIKQI 216
                              |      8        18        28        38        48        58        68        78        88        98       108 ||    118       128|      138       148       158       168       178       188       198       208        
                              1-MSE                                                                                                      110-MSE         126-MSE                                                                                      
                                                                                                                                          111-MSE           129-MSE                                                                                   


Chain C from PDB  Type:PROTEIN  Length:219
 aligned with DAPH_ENTFA | Q836H8 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:219
                              1                                                                                                                                                                                                                        
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208         
           DAPH_ENTFA     - --MDAYEIIQYIGDAKKQTLVKVTLKGQLKEVTFPETIKVFNNCKTGTLFGDWADVKPFLEANKEKIEDYVVENDARNSAIPFLDLKDINARIEPGALIREKVEIGDQAVIMMGAILNIGAVVGAGTMIDMGAVLGGRATVGKHCHIGAGTVLAGVIEPPSAAPVVIENEVVIGANAVVLEGVRVGEGAVVAAGAVVVEDVPAHTVVAGVPAKVIKQID 217
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3cj8C01 C:-1-133cj8C02 C:14-79  [code=3.30.70.250, no name defined]              3cj8C03 C:80-217 Hexapeptide repeat proteins                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh....eeeeeeee...........eeee...eeeeeeehhhhhhhhhhh...eeeeeeee.................ee....ee....ee....ee....ee....ee....ee....ee....ee....ee....ee............ee....ee....ee....ee....ee....ee.......eeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------HEXAPEP_TRANSFERASES         ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cj8 C  -1 NAmDAYEIIQYIGDAKKQTLVKVTLKGQLKEVTFPETIKVFNNCKTGTLFGDWADVKPFLEANKEKIEDYVVENDARNSAIPFLDLKDINARIEPGALIREKVEIGDQAVImmGAILNIGAVVGAGTmIDmGAVLGGRATVGKHCHIGAGTVLAGVIEPPSAAPVVIENEVVIGANAVVLEGVRVGEGAVVAAGAVVVEDVPAHTVVAGVPAKVIKQID 217
                              |      8        18        28        38        48        58        68        78        88        98       108 ||    118       128|      138       148       158       168       178       188       198       208         
                              1-MSE                                                                                                      110-MSE         126-MSE                                                                                       
                                                                                                                                          111-MSE           129-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3CJ8)

(-) CATH Domains  (3, 9)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CJ8)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (DAPH_ENTFA | Q836H8)
molecular function
    GO:0016407    acetyltransferase activity    Catalysis of the transfer of an acetyl group to an acceptor molecule.
    GO:0047200    tetrahydrodipicolinate N-acetyltransferase activity    Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + acetyl-CoA + H(2)O = L-2-acetamido-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.

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  3cj8
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