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(-) Description

Title :  CRYSTAL STRUCTURE OF CITRATE LYASE BETA SUBUNIT
 
Authors :  S. Eswaramoorthy, S. Swaminathan, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgxrc)
Date :  23 Feb 04  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Citrate Lyase Beta Subunit, Trimer, Tim Barrel, Structural Genomics, Psi, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Eswaramoorthy, S. Swaminathan
Crystal Structure Of Citrate Lyase Beta Subunit
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CITRATE LYASE, BETA SUBUNIT
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: DEINOCOCCUS RADIODURANS
    Organism Taxid: 1299

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MG3Ligand/IonMAGNESIUM ION
2OAA3Ligand/IonOXALOACETATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:39 , ARG A:74 , GLU A:129 , TYR A:150 , VAL A:193 , LEU A:219 , ILE A:221 , MG A:286 , HOH A:362 , HOH A:456 , HOH A:470BINDING SITE FOR RESIDUE OAA A 285
2AC2SOFTWAREARG A:74 , GLU A:129 , OAA A:285 , HOH A:287 , HOH A:356BINDING SITE FOR RESIDUE MG A 286
3AC3SOFTWAREARG B:74 , GLU B:129 , VAL B:193 , LEU B:219 , ILE B:221 , MG B:286 , HOH B:585 , HOH B:813BINDING SITE FOR RESIDUE OAA B 285
4AC4SOFTWAREARG B:74 , GLU B:129 , TYR B:150 , OAA B:285 , HOH B:576BINDING SITE FOR RESIDUE MG B 286
5AC5SOFTWAREARG C:74 , GLU C:129 , TYR C:150 , VAL C:193 , ILE C:221 , MG C:286 , HOH C:677 , HOH C:1164BINDING SITE FOR RESIDUE OAA C 285
6AC6SOFTWAREASP C:39 , ARG C:74 , GLU C:129 , TYR C:150 , ASP C:155 , OAA C:285 , HOH C:578BINDING SITE FOR RESIDUE MG C 286

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SGJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SGJ)

(-) 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:231
 aligned with CITEL_DEIRA | Q9RUZ0 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
          CITEL_DEIRA     4 PPALLRSVLFAPGNRADLIAKLPRSAPDAVVIDLEDAVPGTAEAKAAARPVAHDAARDLIAAAPHLAVFVRVNALHSPYFEDDLSVLTPELSGVVVPKLEMGAEARQVAQMLQERSLPLPILAGLETGAGVWNAREIMEVPEVAWAYFGAEDYTTDLGGKRTPGGLEVLYARSQVALAARLTGVAALDIVVTALNDPETFRADAEQGRALGYSGKLCIHPAQVALAHEYFG 234
               SCOP domains d1sgja_ A: Citrate lyase, beta subunit                                                                                                                                                                                                  SCOP domains
               CATH domains 1sgjA00 A:4-234 Phosphoenolpyruvate-binding domains                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..hhhhhhhh......eeeee.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhh.....eeee....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh...eeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sgj A   4 PPALLRSVLFAPGNRADLIAKLPRSAPDAVVIDLEDAVPGTAEAKAAARPVAHDAARDLIAAAPHLAVFVRVNALHSPYFEDDLSVLTPELSGVVVPKLEMGAEARQVAQMLQERSLPLPILAGLETGAGVWNAREIMEVPEVAWAYFGAEDYTTDLGGKRTPGGLEVLYARSQVALAARLTGVAALDIVVTALNDPETFRADAEQGRALGYSGKLCIHPAQVALAHEYFG 234
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with CITEL_DEIRA | Q9RUZ0 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
          CITEL_DEIRA     4 PPALLRSVLFAPGNRADLIAKLPRSAPDAVVIDLEDAVPGTAEAKAAARPVAHDAARDLIAAAPHLAVFVRVNALHSPYFEDDLSVLTPELSGVVVPKLEMGAEARQVAQMLQERSLPLPILAGLETGAGVWNAREIMEVPEVAWAYFGAEDYTTDLGGKRTPGGLEVLYARSQVALAARLTGVAALDIVVTALNDPETFRADAEQGRALGYSGKLCIHPAQVALAHEYFG 234
               SCOP domains d1sgjb_ B: Citrate lyase, beta subunit                                                                                                                                                                                                  SCOP domains
               CATH domains 1sgjB00 B:4-234 Phosphoenolpyruvate-binding domains                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..hhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhh.....eeee....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sgj B   4 PPALLRSVLFAPGNRADLIAKLPRSAPDAVVIDLEDAVPGTAEAKAAARPVAHDAARDLIAAAPHLAVFVRVNALHSPYFEDDLSVLTPELSGVVVPKLEMGAEARQVAQMLQERSLPLPILAGLETGAGVWNAREIMEVPEVAWAYFGAEDYTTDLGGKRTPGGLEVLYARSQVALAARLTGVAALDIVVTALNDPETFRADAEQGRALGYSGKLCIHPAQVALAHEYFG 234
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 


Chain C from PDB  Type:PROTEIN  Length:231
 aligned with CITEL_DEIRA | Q9RUZ0 from UniProtKB/Swiss-Prot  Length:284

    Alignment length:231
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233 
          CITEL_DEIRA     4 PPALLRSVLFAPGNRADLIAKLPRSAPDAVVIDLEDAVPGTAEAKAAARPVAHDAARDLIAAAPHLAVFVRVNALHSPYFEDDLSVLTPELSGVVVPKLEMGAEARQVAQMLQERSLPLPILAGLETGAGVWNAREIMEVPEVAWAYFGAEDYTTDLGGKRTPGGLEVLYARSQVALAARLTGVAALDIVVTALNDPETFRADAEQGRALGYSGKLCIHPAQVALAHEYFG 234
               SCOP domains d1sgjc_ C: Citrate lyase, beta subunit                                                                                                                                                                                                  SCOP domains
               CATH domains 1sgjC00 C:4-234 Phosphoenolpyruvate-binding domains                                                                                                                                                                                     CATH domains
           Pfam domains (1) -----HpcH_HpaI-1sgjC01 C:9-223                                                                                                                                                                                              ----------- Pfam domains (1)
           Pfam domains (2) -----HpcH_HpaI-1sgjC02 C:9-223                                                                                                                                                                                              ----------- Pfam domains (2)
           Pfam domains (3) -----HpcH_HpaI-1sgjC03 C:9-223                                                                                                                                                                                              ----------- Pfam domains (3)
         Sec.struct. author ......eeeeee..hhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee.......hhhhhhh.......eeee....hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhh...eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhhh...eeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sgj C   4 PPALLRSVLFAPGNRADLIAKLPRSAPDAVVIDLEDAVPGTAEAKAAARPVAHDAARDLIAAAPHLAVFVRVNALHSPYFEDDLSVLTPELSGVVVPKLEMGAEARQVAQMLQERSLPLPILAGLETGAGVWNAREIMEVPEVAWAYFGAEDYTTDLGGKRTPGGLEVLYARSQVALAARLTGVAALDIVVTALNDPETFRADAEQGRALGYSGKLCIHPAQVALAHEYFG 234
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: PK_TIM (63)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (CITEL_DEIRA | Q9RUZ0)
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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