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(-) Description

Title :  CRYSTAL STRUCTURE OF CITRATE SYNTHASE FROM PYROBACULUM AEROPHILUM
 
Authors :  D. R. Boutz, T. O. Yeates, D. Cascio
Date :  11 Sep 06  (Deposition) - 15 May 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Disulfide Bond, Homodimer, Citrate Synthase, Thermophilic, Catenane, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Boutz, D. Cascio, J. Whitelegge, L. J. Perry, T. O. Yeates
Discovery Of A Thermophilic Protein Complex Stabilized By Topologically Interlinked Chains.
J. Mol. Biol. V. 368 1332 2007
PubMed-ID: 17395198  |  Reference-DOI: 10.1016/J.JMB.2007.02.078

(-) Compounds

Molecule 1 - CITRATE SYNTHASE
    Chains: A, B
    EC Number: 2.3.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETM11
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PAE1689
    Organism Scientific: PYROBACULUM AEROPHILUM
    Organism Taxid: 178306
    Strain: IM2

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO B:359 , TYR B:360 , HOH B:1246 , HOH B:1271BINDING SITE FOR RESIDUE ACT B 901
2AC2SOFTWAREPRO A:359 , TYR A:360 , HOH A:928BINDING SITE FOR RESIDUE ACT A 902
3AC3SOFTWAREGLU B:304 , ASP B:308 , HOH B:914 , HOH B:1177 , HOH B:1202 , HOH B:1283 , HOH B:1284BINDING SITE FOR RESIDUE MG B 903
4AC4SOFTWAREASP A:308 , HOH A:1064 , HOH A:1167 , HOH A:1299 , HOH A:1300 , HOH A:1301 , HOH A:1302BINDING SITE FOR RESIDUE MG A 904

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:19 -A:394
2B:19 -B:394

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:279 -Gly A:280
2Gly A:280 -Gly A:281
3Gly A:281 -Pro A:282

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IBP)

(-) 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:407
 aligned with Q8ZWP2_PYRAE | Q8ZWP2 from UniProtKB/TrEMBL  Length:409

    Alignment length:407
                                    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       
         Q8ZWP2_PYRAE     3 EQTVQVKTTGKILQSPCGPIIHGLEDVLIKSTSISDIDGEKGILWYRGYRIEELARLSTYEEVSYLILYGRLPTKRELEDYINRMKKYRELHPATVEVIRNLAKAHPMFALEAAVAAEGAYDEDNQKLIEALSVGRYKAEEKELAYRIAEKLVAKMPTIVAYHYRFSRGLEVVRPRDDLGHAANFLYMMFGREPDPLASRGIDLYLILHADHEVPASTFAAHVVASTLSDLYSSVAAAIAALKGPLHGGANEMAVRNYLEIGTPAKAKEIVEAATKPGGPKLMGVGHRVYKAYDPRAKIFKEFSRDYVAKFGDPQNLFAIASAIEQEVLSHPYFQQRKLYPNVDFWSGIAFYYMGIPYEYFTPIFAMSRVVGWVAHVLEYWENNRIFRPRACYIGPHDLQYIPLEQR 409
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...ee......ee.hhh..eeeee..eeee....eeee..eehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.........hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ibp A   3 EQTVQVKTTGKILQSPCGPIIHGLEDVLIKSTSISDIDGEKGILWYRGYRIEELARLSTYEEVSYLILYGRLPTKRELEDYINRMKKYRELHPATVEVIRNLAKAHPMFALEAAVAAEGAYDEDNQKLIEALSVGRYKAEEKELAYRIAEKLVAKMPTIVAYHYRFSRGLEVVRPRDDLGHAANFLYMMFGREPDPLASRGIDLYLILHADHEVPASTFAAHVVASTLSDLYSSVAAAIAALKGPLHGGANEMAVRNYLEIGTPAKAKEIVEAATKPGGPKLMGVGHRVYKAYDPRAKIFKEFSRDYVAKFGDPQNLFAIASAIEQEVLSHPYFQQRKLYPNVDFWSGIAFYYMGIPYEYFTPIFAMSRVVGWVAHVLEYWENNRIFRPRACYIGPHDLQYIPLEQR 409
                                    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       


Chain B from PDB  Type:PROTEIN  Length:407
 aligned with Q8ZWP2_PYRAE | Q8ZWP2 from UniProtKB/TrEMBL  Length:409

    Alignment length:407
                                    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       
         Q8ZWP2_PYRAE     3 EQTVQVKTTGKILQSPCGPIIHGLEDVLIKSTSISDIDGEKGILWYRGYRIEELARLSTYEEVSYLILYGRLPTKRELEDYINRMKKYRELHPATVEVIRNLAKAHPMFALEAAVAAEGAYDEDNQKLIEALSVGRYKAEEKELAYRIAEKLVAKMPTIVAYHYRFSRGLEVVRPRDDLGHAANFLYMMFGREPDPLASRGIDLYLILHADHEVPASTFAAHVVASTLSDLYSSVAAAIAALKGPLHGGANEMAVRNYLEIGTPAKAKEIVEAATKPGGPKLMGVGHRVYKAYDPRAKIFKEFSRDYVAKFGDPQNLFAIASAIEQEVLSHPYFQQRKLYPNVDFWSGIAFYYMGIPYEYFTPIFAMSRVVGWVAHVLEYWENNRIFRPRACYIGPHDLQYIPLEQR 409
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...ee......ee.hhh..eeeee..eeee....eeee..eehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.........hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ibp B   3 EQTVQVKTTGKILQSPCGPIIHGLEDVLIKSTSISDIDGEKGILWYRGYRIEELARLSTYEEVSYLILYGRLPTKRELEDYINRMKKYRELHPATVEVIRNLAKAHPMFALEAAVAAEGAYDEDNQKLIEALSVGRYKAEEKELAYRIAEKLVAKMPTIVAYHYRFSRGLEVVRPRDDLGHAANFLYMMFGREPDPLASRGIDLYLILHADHEVPASTFAAHVVASTLSDLYSSVAAAIAALKGPLHGGANEMAVRNYLEIGTPAKAKEIVEAATKPGGPKLMGVGHRVYKAYDPRAKIFKEFSRDYVAKFGDPQNLFAIASAIEQEVLSHPYFQQRKLYPNVDFWSGIAFYYMGIPYEYFTPIFAMSRVVGWVAHVLEYWENNRIFRPRACYIGPHDLQYIPLEQR 409
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 2IBP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IBP)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8ZWP2_PYRAE | Q8ZWP2)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0046912    transferase activity, transferring acyl groups, acyl groups converted into alkyl on transfer    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor), with the acyl group being converted into alkyl on transfer.
biological process
    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.

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