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(-) Description

Title :  STRUCTURE OF CITRATE LYASE BETA SUBUNIT FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  C. W. Goulding, T. Lekin, C. Y. Kim, B. Segelke, T. C. Terwilliger, D. Eisenberg, Tb Structural Genomics Consortium (Tbsgc)
Date :  27 Jul 04  (Deposition) - 12 Oct 04  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CITE
    Chains: A
    EC Number: 4.1.3.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI K12
    Expression System Plasmid: PET
    Expression System Strain: K12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Gene: RV2498C
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: CITRATE LYASE BETA SUBUNIT

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:157 , ARG A:160BINDING SITE FOR RESIDUE FMT A 274

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U5H)

(-) 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 1U5H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U5H)

(-) Exons   (0, 0)

(no "Exon" information available for 1U5H)

(-) 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:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
          CITEL_MYCTO     1 MNLRAAGPGWLFCPADRPERFAKAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVMLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAYRPSHEKLAWARRVLAA 237
               SCOP domains d1u5ha_ A: Citrate lyase, beta subunit                                                                                                                                                                                                        SCOP domains
               CATH domains 1u5hA00 A:1-223 Phosphoenolpyruvate-binding domains                                                                                                                                                                                           CATH domains
               Pfam domains ---------HpcH_HpaI-1u5hA01 A:10-211                                                                                                                                                                                -------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh....eeee....hhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeeehhhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh--------------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5h A   1 MNLRAAGPGWLFCPADAPEAFAAAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVMLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAY--------------AA 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220|        -     | 
                                                                                                                                                                                                                                                      221            222 


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

    Alignment length:237
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
          CITEL_MYCTU     1 MNLRAAGPGWLFCPADRPERFAKAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVMLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAYRPSHEKLAWARRVLAA 237
               SCOP domains d1u5ha_ A: Citrate lyase, beta subunit                                                                                                                                                                                                        SCOP domains
               CATH domains 1u5hA00 A:1-223 Phosphoenolpyruvate-binding domains                                                                                                                                                                                           CATH domains
               Pfam domains ---------HpcH_HpaI-1u5hA01 A:10-211                                                                                                                                                                                -------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhh.eeeee.....hhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhh....eeee....hhhhhhh....eeeeee.hhhhhhhhhhhhhh..eeeeeehhhhhhhhhh...........hhhhhhhhhhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhh--------------.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u5h A   1 MNLRAAGPGWLFCPADAPEAFAAAAAAADVVILDLEDGVAEAQKPAARNALRDTPLDPERTVVRINAGGTADQARDLEALAGTAYTTVMLPKAESAAQVIELAPRDVIALVETARGAVCAAEIAAADPTVGMMWGAEDLIATLGGSSSRRADGAYRDVARHVRSTILLAASAFGRLALDAVHLDILDVEGLQEEARDAAAVGFDVTVCIHPSQIPVVRKAY--------------AA 223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220|        -     | 
                                                                                                                                                                                                                                                      221            222
   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_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.

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.

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  1u5h
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  CITEL_MYCTU | P9WPE1
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 Related Entries

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

UniProtKB/Swiss-Prot
        CITEL_MYCTO | P9WPE0: 1u5v 1z6k
        CITEL_MYCTU | P9WPE1: 1u5v 1z6k

(-) Related Entries Specified in the PDB File

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