Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - 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 :  CITRATE LYASE BETA SUBUNIT COMPLEXED WITH OXALOACETATE AND MAGNESIUM FROM M. TUBERCULOSIS
 
Authors :  C. W. Goulding, P. M. Bowers, B. Segelke, T. Lekin, C. Y. Kim, T. C. Terwil D. Eisenberg, Tb Structural Genomics Consortium (Tbsgc)
Date :  22 Mar 05  (Deposition) - 03 May 05  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Tim Barrel, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. W. Goulding, P. M. Bowers, B. Segelke, T. Lekin, C. Y. Kim, T. C. Terwilliger, D. Eisenberg
The Structure And Computational Analysis Of Mycobacterium Tuberculosis Protein Cite Suggest A Novel Enzymatic Function.
J. Mol. Biol. V. 365 275 2007
PubMed-ID: 17064730  |  Reference-DOI: 10.1016/J.JMB.2006.09.086

(-) Compounds

Molecule 1 - CITRATE LYASE BETA SUBUNIT
    Chains: A
    EC Number: 4.1.3.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28D+
    Expression System Strain: BL21(DE3)PRO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RV2498C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2MSE4Mod. Amino AcidSELENOMETHIONINE
3OAA1Ligand/IonOXALOACETATE ION
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE12Mod. Amino AcidSELENOMETHIONINE
3OAA3Ligand/IonOXALOACETATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:36 , ARG A:64 , GLU A:112 , MG A:275BINDING SITE FOR RESIDUE OAA A 274
2AC2SOFTWAREGLU A:112 , ASP A:138 , OAA A:274 , HOH A:297BINDING SITE FOR RESIDUE MG A 275

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z6K)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:103 -Pro A:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z6K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z6K)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z6K)

(-) 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:223
 aligned with CITEL_MYCTO | P9WPE0 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
          CITEL_MYCTO     1 MNLRAAGPGWLFCPADRPERFAKAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVMLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAYRP 223
               SCOP domains d1z6ka_ A: Citrate lyase, beta subunit                                                                                                                                                                                          SCOP domains
               CATH domains -1z6kA00 A:2-223 Phosphoenolpyruvate-binding domains                                                                                                                                                                            CATH domains
               Pfam domains ---------HpcH_HpaI-1z6kA01 A:10-211                                                                                                                                                                                ------------ Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhh.eeeee........hhhhhhhhhhhh......eeee.....hhhhhhhhhhhh.....eeee....hhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeeehhhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z6k A   1 mNLRAAGPGWLFCPADRPERFAKAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVmLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGmmWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAYRP 223
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130 ||    140       150       160       170       180       190       200       210       220   
                            |                                                                                      89-MSE                                    132-MSE                                                                                       
                            1-MSE                                                                                                                             133-MSE                                                                                      


Chain A from PDB  Type:PROTEIN  Length:223
 aligned with CITEL_MYCTU | P9WPE1 from UniProtKB/Swiss-Prot  Length:273

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
          CITEL_MYCTU     1 MNLRAAGPGWLFCPADRPERFAKAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVMLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAYRP 223
               SCOP domains d1z6ka_ A: Citrate lyase, beta subunit                                                                                                                                                                                          SCOP domains
               CATH domains -1z6kA00 A:2-223 Phosphoenolpyruvate-binding domains                                                                                                                                                                            CATH domains
               Pfam domains ---------HpcH_HpaI-1z6kA01 A:10-211                                                                                                                                                                                ------------ Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhh.eeeee........hhhhhhhhhhhh......eeee.....hhhhhhhhhhhh.....eeee....hhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeeehhhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z6k A   1 mNLRAAGPGWLFCPADRPERFAKAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVmLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGmmWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAYRP 223
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130 ||    140       150       160       170       180       190       200       210       220   
                            1-MSE                                                                                  89-MSE                                    132-MSE                                                                                       
                                                                                                                                                              133-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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PK_TIM (63)

(-) Gene Ontology  (5, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (CITEL_MYCTO | P9WPE0)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

Chain A   (CITEL_MYCTU | P9WPE1)
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.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0006107    oxaloacetate metabolic process    The chemical reactions and pathways involving oxaloacetate, the anion of oxobutanedioic acid, an important intermediate in metabolism, especially as a component of 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
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OAA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:103 - Pro A:104   [ 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
  1z6k
    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
  CITEL_MYCTO | P9WPE0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  CITEL_MYCTU | P9WPE1
    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)
  4.1.3.6
    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
  CITEL_MYCTO | P9WPE0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  CITEL_MYCTU | P9WPE1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CITEL_MYCTO | P9WPE0: 1u5h 1u5v
        CITEL_MYCTU | P9WPE1: 1u5h 1u5v

(-) Related Entries Specified in the PDB File

1sgj CITE FROM D. RADIODURANS RELATED ID: RV2498C RELATED DB: TARGETDB
1u5h APO-CITE FROM M. TUBERCULOSIS