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

(-) Description

Title :  2.4 ANGSTROM CRYSTAL STRUCTURE OF FUMARATE HYDRATASE FROM RICKETTSIA PROWAZEKII
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  27 Mar 09  (Deposition) - 14 Jul 09  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Structural Genomics, Ssgcid, Fumarate, Hydratase, Lyase, Tricarboxylic Acid Cycle, Seattle Structural Genomics Center For Infectious Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Phan, S. Subramanian, C. Olsen, T. E. Edwards, W. Guo, Y. Zhang, W. C. Van Voorhis, L. J. Stewart, P. J. Myler
Structure Of Fumarate Hydratase From Rickettsia Prowazekii, The Agent Of Typhus And Suspected Relative Of The Mitochondria.
Acta Crystallogr. , Sect. F V. 67 1123 2011
PubMed-ID: 21904061  |  Reference-DOI: 10.1107/S174430911102690X

(-) Compounds

Molecule 1 - FUMARATE HYDRATASE CLASS II
    Chains: A, B
    EC Number: 4.2.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FUMC, RP665
    Organism Scientific: RICKETTSIA PROWAZEKII
    Organism Taxid: 272947
    Strain: MADRID-E
    Synonym: FUMARASE C

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1MLI2Ligand/IonMALONATE ION
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MLI4Ligand/IonMALONATE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:98 , THR A:100 , ASN A:141 , THR B:187 , HIS B:188 , MET B:321 , LYS B:324 , ASN B:326BINDING SITE FOR RESIDUE MLI A 462
2AC2SOFTWAREGLN A:339 , ASN A:343 , HOH A:538 , HOH A:546 , GLN B:339 , ASN B:343 , HOH B:537 , HOH B:542BINDING SITE FOR RESIDUE NA A 463
3AC3SOFTWARETHR A:187 , HIS A:188 , GLY A:317 , SER A:318 , LYS A:324 , ASN A:326 , SER B:98 , THR B:100 , SER B:140 , ASN B:141BINDING SITE FOR RESIDUE MLI B 462

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:126 -Pro A:127
2Gly A:301 -Pro A:302
3Phe B:126 -Pro B:127
4Gly B:301 -Pro B:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.FUMC_RICPR317-326
 		  2A:317-326
B:321-326
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FUMARATE_LYASESPS00163 Fumarate lyases signature.FUMC_RICPR317-326
 		  4A:317-326
B:321-326

(-) Exons   (0, 0)

(no "Exon" information available for 3GTD)

(-) 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:455
 aligned with FUMC_RICPR | Q9ZCQ4 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:455
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452     
           FUMC_RICPR     3 NYRIESDSFGEIQIEEKFYWGAQTQRSLNNFKISKQKMPKILIRALAILKKCAAQVNYEFGDLEYKIATSIDKAIDRILAGEFEDNFPLVVWQTGSGTQTNMNMNEVIASIANEELTGKKGGKFPVHPNDHVNKGQSSNDSFPTAMHIATVLATKQQLIPALNNLLTYLQDKSKDWDKIIKIGRTHLQDATPLTLKQEFSGYITQIEYALERIEDALKKVYLLAQGGTAVGTGINSKIGFDIKFAQKVAEFTQQPFKTAPNKFESLAAHDALVEFSGTLNTIAVSLMKIANDIRLLGSGPRCGLGELHLPENEPGSSIMPGKVNPTQVEALTMVCTQVMGNHVTVTIAGSNGHLELNVFKPVIIYNILQSIELLSDSVNSFVTHCVKGLEPNIARINTLRDKSLMLVTVLNPHIGYDNAAKIAKEAHKYGITLKEAAKKLNFLSEEEFDKIVVPE 457
               SCOP domains d3gtda_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --3gtdA01 A:5-138 Fumarase/aspartase (N-terminal domain)                                                                                3gtdA02 A:139-407 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                        3gtdA03 A:408-455                               -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh...ee...............hhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee................hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gtd A   3 NYRIESDSFGEIQIEEKFYWGAQTQRSLNNFKISKQKMPKILIRALAILKKCAAQVNYEFGDLEYKIATSIDKAIDRILAGEFEDNFPLVVWQTGSGTQTNMNMNEVIASIANEELTGKKGGKFPVHPNDHVNKGQSSNDSFPTAMHIATVLATKQQLIPALNNLLTYLQDKSKDWDKIIKIGRTHLQDATPLTLKQEFSGYITQIEYALERIEDALKKVYLLAQGGTAVGTGINSKIGFDIKFAQKVAEFTQQPFKTAPNKFESLAAHDALVEFSGTLNTIAVSLMKIANDIRLLGSGPRCGLGELHLPENEPGSSIMPGKVNPTQVEALTMVCTQVMGNHVTVTIAGSNGHLELNVFKPVIIYNILQSIELLSDSVNSFVTHCVKGLEPNIARINTLRDKSLMLVTVLNPHIGYDNAAKIAKEAHKYGITLKEAAKKLNFLSEEEFDKIVVPE 457
                                    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       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452     


Chain B from PDB  Type:PROTEIN  Length:400
 aligned with FUMC_RICPR | Q9ZCQ4 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:404
                                    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       302       312       322       332       342       352       362       372       382       392       402    
           FUMC_RICPR     3 NYRIESDSFGEIQIEEKFYWGAQTQRSLNNFKISKQKMPKILIRALAILKKCAAQVNYEFGDLEYKIATSIDKAIDRILAGEFEDNFPLVVWQTGSGTQTNMNMNEVIASIANEELTGKKGGKFPVHPNDHVNKGQSSNDSFPTAMHIATVLATKQQLIPALNNLLTYLQDKSKDWDKIIKIGRTHLQDATPLTLKQEFSGYITQIEYALERIEDALKKVYLLAQGGTAVGTGINSKIGFDIKFAQKVAEFTQQPFKTAPNKFESLAAHDALVEFSGTLNTIAVSLMKIANDIRLLGSGPRCGLGELHLPENEPGSSIMPGKVNPTQVEALTMVCTQVMGNHVTVTIAGSNGHLELNVFKPVIIYNILQSIELLSDSVNSFVTHCVKGLEPNIARINTLRDKSL 406
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --3gtdB01 B:5-138 Fumarase/aspartase (N-terminal domain)                                                                                3gtdB02 B:139-406 Fumarase/aspartase (Central domain)                                                                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeee.....hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhh...ee...............hhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........ee......----......hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L-------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gtd B   3 NYRIESDSFGEIQIEEKFYWGAQTQRSLNNFKISKQKMPKILIRALAILKKCAAQVNYEFGDLEYKIATSIDKAIDRILAGEFEDNFPLVVWQTGSGTQTNMNMNEVIASIANEELTGKKGGKFPVHPNDHVNKGQSSNDSFPTAMHIATVLATKQQLIPALNNLLTYLQDKSKDWDKIIKIGRTHLQDATPLTLKQEFSGYITQIEYALERIEDALKKVYLLAQGGTAVGTGINSKIGFDIKFAQKVAEFTQQPFKTAPNKFESLAAHDALVEFSGTLNTIAVSLMKIANDIRLLGSGPRCGLGELHLPENEP----MPGKVNPTQVEALTMVCTQVMGNHVTVTIAGSNGHLELNVFKPVIIYNILQSIELLSDSVNSFVTHCVKGLEPNIARINTLRDKSL 406
                                    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       302       312   |   322       332       342       352       362       372       382       392       402    
                                                                                                                                                                                                                                                                                                                                                   316  321
   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: All alpha proteins (14657)

(-) CATH Domains  (3, 5)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FUMC_RICPR | Q9ZCQ4)
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:0004333    fumarate hydratase activity    Catalysis of the reaction: (S)-malate = fumarate + H(2)O.
    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:0006106    fumarate metabolic process    The chemical reactions and pathways involving fumarate, the anion of trans-1,2-ethenedicarboxylic acid, the diastereoisomer of maleate. It is a key intermediate in metabolism and is formed in the TCA cycle from succinate and converted into malate.
    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.
    GO:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0045239    tricarboxylic acid cycle enzyme complex    Any of the heteromeric enzymes that act in the TCA cycle.

 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
    MLI  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:301 - Pro A:302   [ RasMol ]  
    Gly B:301 - Pro B:302   [ RasMol ]  
    Phe A:126 - Pro A:127   [ RasMol ]  
    Phe B:126 - Pro B:127   [ 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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  3gtd
    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
  FUMC_RICPR | Q9ZCQ4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.2.1.2
    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
  FUMC_RICPR | Q9ZCQ4
    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 3GTD)

(-) Related Entries Specified in the PDB File

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