Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE DIHYDRODIPICOLINATE SYNTHASE (TTHA0737) FROM THERMUS THERMOPHILUS HB8
 
Authors :  J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, Y. Kitamu A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken St Genomics/Proteomics Initiative (Rsgi)
Date :  30 Mar 07  (Deposition) - 02 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Lyase, Lysine Biosynthesis, Synthase, Dihydrodipicoliante, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, Y. Kitamura, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of Putative Dihydrodipicolinate Synthase (Ttha0737) From Thermus Thermophilus Hb8
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE DIHYDRODIPICOLINATE SYNTHASE
    Chains: A
    EC Number: 4.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: B834(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2K1Ligand/IonPOTASSIUM ION
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL
2K-1Ligand/IonPOTASSIUM ION
3MSE16Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2PCQ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PCQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:257 -Pro A:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PCQ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PCQ)

(-) Exons   (0, 0)

(no "Exon" information available for 2PCQ)

(-) 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:283
 aligned with Q5SKB1_THET8 | Q5SKB1 from UniProtKB/TrEMBL  Length:283

    Alignment length:283
                                    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   
         Q5SKB1_THET8     1 MILPPIPTPFDREGRLDEEAFRELAQALEPLVDGLLVYGSNGEGVHLTPEERARGLRALRPRKPFLVGLMEETLPQAEGALLEAKAAGAMALLATPPRYYHGSLGAGLLRYYEALAEKMPLFLYHVPQNTKVDLPLEAVEALAPHPNVLGIKDSSGDLSRIAFYQARLQEFRVYTGHAPTFLGALALGAEGGILAAANLAPRAYRALLDHFREGRLAEAQELQKKLFPLGDLLAKGGVPLLKQALRHLGLPAGYPRPPYPAESPLWERFLPVLEGLKEEGWVL 283
               SCOP domains d2pcqa_ A: automated matches                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains DHDPS-2pcqA01 A:1-266                                                                                                                                                                                                                                                     ----------------- Pfam domains
         Sec.struct. author .ee.ee..........hhhhhhhhhhhhhhhh...ee.....hhhhhhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhh.eeeeehhhhhh...hhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeee.hhhhhhhhhhh...eee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pcq A   1 mILPPIPTPFDREGRLDEEAFRELAQALEPLVDGLLVYGSNGEGVHLTPEERARGLRALRPRKPFLVGLmEETLPQAEGALLEAKAAGAmALLATPPRYYHGSLGAGLLRYYEALAEKmPLFLYHVPQNTKVDLPLEAVEALAPHPNVLGIKDSSGDLSRIAFYQARLQEFRVYTGHAPTFLGALALGAEGGILAAANLAPRAYRALLDHFREGRLAEAQELQKKLFPLGDLLAKGGVPLLKQALRHLGLPAGYPRPPYPAESPLWERFLPVLEGLKEEGWVL 283
                            |       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   
                            |                                                                   70-MSE              90-MSE                      119-MSE                                                                                                                                                                
                            1-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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2PCQ)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5SKB1_THET8 | Q5SKB1)
molecular function
    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: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.

 Visualization

(-) Interactive Views

Asymmetric 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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 2pcq)
 
  Cis Peptide Bonds
    Pro A:257 - Pro A:258   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  2pcq
    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
  Q5SKB1_THET8 | Q5SKB1
    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)
  4.2.1.52
    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
  Q5SKB1_THET8 | Q5SKB1
    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 2PCQ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2PCQ)