Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF A 2,3,4,5-TETRAHYDROPYRIDINE-2,6-DICARBOXYLATE N-SUCCINYLTRANSFERASE FROM BURKHOLDERIA PSEUDOMALLEI
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  25 Aug 11  (Deposition) - 12 Oct 11  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ssgcid, Seattle Structural Genomics Center For Infectious Disease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Clifton, A. Gardberg, Seattle Structural Genomics Center For Infectious Disease (Ssgcid)
Structure Of A 2, 3, 4, 5-Tetrahydropyridine-2, 6-Dicarboxylate N-Succinyltransferase From Burkholderia Pseudomallei
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 2,3,4,5-TETRAHYDROPYRIDINE-2,6-DICARBOXYLATE N- SUCCINYLTRANSFERASE
    Chains: A, B, C
    EC Number: 2.3.1.117
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DAPD, BURPS1710B_2594
    Organism Scientific: BURKHOLDERIA PSEUDOMALLEI
    Organism Taxid: 320372
    Strain: 1710B

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric/Biological Unit (3, 24)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2SO414Ligand/IonSULFATE ION
3UNL4Ligand/IonUNKNOWN LIGAND

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:151 , ASN A:168 , SER A:187 , HOH A:406 , HOH A:940BINDING SITE FOR RESIDUE EDO A 313
02AC2SOFTWAREASP A:180 , THR A:181 , GLY A:199 , HOH A:330 , HOH A:341 , HOH A:428 , HOH A:475 , HOH B:352 , HOH B:369BINDING SITE FOR RESIDUE SO4 A 314
03AC3SOFTWAREGLN A:43 , VAL A:93 , HIS A:94 , GLN A:95 , TRP A:96 , HOH A:359 , HOH A:920BINDING SITE FOR RESIDUE SO4 A 315
04AC4SOFTWARETHR A:133 , ALA A:134 , GLU A:135 , LYS C:280BINDING SITE FOR RESIDUE SO4 A 316
05AC5SOFTWARESER A:62 , ALA A:63 , ARG A:66 , HOH A:390BINDING SITE FOR RESIDUE SO4 A 317
06AC6SOFTWAREASN A:110 , LYS A:124 , HOH A:441 , HOH A:460 , HOH A:481 , HOH A:836 , ARG C:143BINDING SITE FOR RESIDUE SO4 A 318
07AC7SOFTWAREGLY A:89 , ALA A:90 , TRP A:91 , ARG A:265 , HOH A:485 , HOH A:636BINDING SITE FOR RESIDUE SO4 A 319
08AC8SOFTWAREASN A:52 , LYS A:193 , HOH A:379BINDING SITE FOR RESIDUE EDO A 320
09AC9SOFTWAREPRO A:209 , LEU A:210 , GLN A:211BINDING SITE FOR RESIDUE EDO A 321
10BC1SOFTWAREGLN A:40 , GLN A:44 , ASN A:159 , GLY A:176 , ASN A:194BINDING SITE FOR RESIDUE EDO A 324
11BC2SOFTWAREARG B:151 , ASN B:168 , SER B:187 , HOH B:362 , HOH B:365BINDING SITE FOR RESIDUE EDO B 313
12BC3SOFTWAREASP B:180 , THR B:181 , GLY B:199 , HOH B:323 , HOH B:345 , HOH B:347 , HOH B:376 , HOH B:511 , HOH B:961 , THR C:184 , HOH C:322 , HOH C:349BINDING SITE FOR RESIDUE SO4 B 314
13BC4SOFTWAREGLN B:43 , VAL B:93 , HIS B:94 , GLN B:95 , TRP B:96 , HOH B:367 , HOH B:396BINDING SITE FOR RESIDUE SO4 B 315
14BC5SOFTWARELYS A:280 , THR B:133 , ALA B:134 , HOH B:422 , HOH B:893BINDING SITE FOR RESIDUE SO4 B 316
15BC6SOFTWARESER B:62 , ALA B:63 , HOH B:497BINDING SITE FOR RESIDUE SO4 B 317
16BC7SOFTWARETHR A:184 , HOH A:338 , HOH A:917 , ASP C:180 , THR C:181 , GLY C:199 , HOH C:325 , HOH C:364 , HOH C:391 , HOH C:907BINDING SITE FOR RESIDUE SO4 C 313
17BC8SOFTWAREGLN C:43 , VAL C:93 , HIS C:94 , GLN C:95 , TRP C:96 , HOH C:918 , HOH C:919BINDING SITE FOR RESIDUE SO4 C 314
18BC9SOFTWARELYS B:280 , THR C:133 , ALA C:134 , HOH C:518BINDING SITE FOR RESIDUE SO4 C 315
19CC1SOFTWARETRP C:50 , ARG C:53BINDING SITE FOR RESIDUE SO4 C 316
20CC2SOFTWARETYR A:287 , SER C:242 , MET C:243 , VAL C:273 , ALA C:274BINDING SITE FOR RESIDUE EDO C 317

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TK8)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Pro A:146 -Pro A:147
2Glu A:208 -Pro A:209
3Pro B:146 -Pro B:147
4Glu B:208 -Pro B:209
5Pro C:146 -Pro C:147
6Glu C:208 -Pro C:209

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TK8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TK8)

(-) Exons   (0, 0)

(no "Exon" information available for 3TK8)

(-) 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:261
 aligned with Q3JR17_BURP1 | Q3JR17 from UniProtKB/TrEMBL  Length:312

    Alignment length:261
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296 
         Q3JR17_BURP1    37 NMSQQLQQIIDNAWENRAELSPKAASAEIREAVAHAIEQLDRGALRVAEKIDGAWTVHQWLKKAVLLSFRLEDNAPMPAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKNVVLMPSYTNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDNCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPAKDGTHSLYCAVIVKKVDA 297
               SCOP domains d3tk8a_ A: automated matches                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhh...eeee.....eeee.........hhhhhhhhh.ee....ee....ee....ee..eee....ee....ee...eee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee.....ee..ee...eeeeeeeee......eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tk8 A  37 NMSQQLQQIIDNAWENRAELSPKAASAEIREAVAHAIEQLDRGALRVAEKIDGAWTVHQWLKKAVLLSFRLEDNAPMPAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKNVVLMPSYTNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDNCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPAKDGTHSLYCAVIVKKVDA 297
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296 


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with Q3JR17_BURP1 | Q3JR17 from UniProtKB/TrEMBL  Length:312

    Alignment length:257
                                    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       
         Q3JR17_BURP1    39 SQQLQQIIDNAWENRAELSPKAASAEIREAVAHAIEQLDRGALRVAEKIDGAWTVHQWLKKAVLLSFRLEDNAPMPAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKNVVLMPSYTNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDNCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPAKDGTHSLYCAVIVKKV 295
               SCOP domains d3tk8b_ B: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....eeee..eeeehhhhhhhhhhhhhh...eeee.....eeee.........hhhhhhhhh.ee....ee....ee....ee..eee....ee....ee...eee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee.....ee..ee...eeeeeeeee......eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tk8 B  39 SQQLQQIIDNAWENRAELSPKAASAEIREAVAHAIEQLDRGALRVAEKIDGAWTVHQWLKKAVLLSFRLEDNAPMPAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKNVVLMPSYTNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDNCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPAKDGTHSLYCAVIVKKV 295
                                    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       


Chain C from PDB  Type:PROTEIN  Length:258
 aligned with Q3JR17_BURP1 | Q3JR17 from UniProtKB/TrEMBL  Length:312

    Alignment length:258
                                    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        
         Q3JR17_BURP1    39 SQQLQQIIDNAWENRAELSPKAASAEIREAVAHAIEQLDRGALRVAEKIDGAWTVHQWLKKAVLLSFRLEDNAPMPAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKNVVLMPSYTNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDNCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPAKDGTHSLYCAVIVKKVD 296
               SCOP domains d3tk8c_ C: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.....eehhhhh.eehhhhhhhhhhhhhh...eeee.....eeee.........hhhhhhhhh.ee....ee....ee....ee..eee....ee....ee...eee....ee....ee....ee............ee....ee....ee....ee....ee....ee.....eee.....ee..ee...eeeeeeeee......eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tk8 C  39 SQQLQQIIDNAWENRAELSPKAASAEIREAVAHAIEQLDRGALRVAEKIDGAWTVHQWLKKAVLLSFRLEDNAPMPAGGYSQFYDKVPSKFANYTAEDFAAGGFRVVPPAIARRGSFIAKNVVLMPSYTNIGAYVDEGTMVDTWATVGSCAQIGKNVHLSGGVGIGGVLEPLQANPVIIEDNCFIGARSEVVEGVIVEENSVISMGVYLGQSTKIYDRETGEVTYGRIPAGSVVVAGNLPAKDGTHSLYCAVIVKKVD 296
                                    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
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TK8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TK8)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Q3JR17_BURP1 | Q3JR17)
molecular function
    GO:0008666    2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity    Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H(2)O + succinyl-CoA = L-2-succinylamino-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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:208 - Pro A:209   [ RasMol ]  
    Glu B:208 - Pro B:209   [ RasMol ]  
    Glu C:208 - Pro C:209   [ RasMol ]  
    Pro A:146 - Pro A:147   [ RasMol ]  
    Pro B:146 - Pro B:147   [ RasMol ]  
    Pro C:146 - Pro C:147   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3tk8
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q3JR17_BURP1 | Q3JR17
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.3.1.117
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q3JR17_BURP1 | Q3JR17
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3TK8)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3TK8)