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(-) Description

Title :  CRYSTAL STRUCTURE OF PUTATIVE LONG-CHAIN-FATTY-ACID COA LIGASE FROM RHODOPSEUDOMONAS PALUSTRIS CGA009
 
Authors :  Y. Patskovsky, R. Toro, R. Foti, M. Dickey, J. M. Sauder, S. K. Burley, S. New York Sgx Research Center For Structural Genomics (Nysgx
Date :  01 Sep 09  (Deposition) - 08 Sep 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-2, Fatty Acid Coa-Ligase, Protein Structure Initiative, Fatty Acid Synthesis, New York Sgx Research Center For Structural Genomics, Nysgxrc, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Patskovsky, R. Toro, R. Foti, M. Dickey, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of Putative Long-Chain-Fatty-Acid Coa Synthase From Rhodopseudomonas Palustris Cga009
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE LONG-CHAIN-FATTY-ACID COA LIGASE
    Chains: A, B
    EC Number: 6.2.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: FADD1, RPA1242
    Organism Scientific: RHODOPSEUDOMONAS PALUSTRIS
    Organism Taxid: 1076

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL6Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:363 , ASN A:364 , ALA A:366 , HOH A:567 , HOH A:642BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREPHE A:7 , ALA A:160 , GLY A:184 , HOH A:518 , HOH A:701 , TRP B:330 , PRO B:356 , HOH B:712BINDING SITE FOR RESIDUE GOL A 511
3AC3SOFTWAREGLY A:280 , LEU A:281 , ASP A:282 , ILE A:287 , ALA A:301 , THR A:302 , SER A:323 , HOH A:532BINDING SITE FOR RESIDUE GOL A 512
4AC4SOFTWAREPRO A:327 , ARG A:331 , THR A:332 , VAL A:333 , HOH A:548 , HOH A:609 , HOH A:653 , ARG B:14 , ARG B:15BINDING SITE FOR RESIDUE GOL A 513
5AC5SOFTWARETRP A:330 , PRO A:356 , PHE B:7 , ALA B:160 , GLY B:184 , LEU B:187 , HOH B:712 , HOH B:713BINDING SITE FOR RESIDUE GOL B 1
6AC6SOFTWAREGLY B:280 , LEU B:281 , ASP B:282 , PHE B:299 , ALA B:301 , THR B:302 , TYR B:317 , SER B:323 , HOH B:531BINDING SITE FOR RESIDUE GOL B 511
7AC7SOFTWAREHOH A:526 , VAL B:333BINDING SITE FOR RESIDUE CL B 512

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:257 -Pro A:258
2Ala B:257 -Pro B:258

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IVR)

(-) Exons   (0, 0)

(no "Exon" information available for 3IVR)

(-) 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:394
 aligned with Q6NAE3_RHOPA | Q6NAE3 from UniProtKB/TrEMBL  Length:503

    Alignment length:396
                                    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      
         Q6NAE3_RHOPA     3 ALHDFTLADVYRRNAALFPDRTAFMVDGVRLTHRDYLARAERLASGLLRDGVHTGDRVAILSQNCSEMIELIGAVALIGAILLPVNYRLNADEIAFVLGDGAPSVVVAGTDYRDIVAGVLPSLGGVKKAYAIGDGSGPFAPFKDLASDTPFSAPEFGAADGFVIIHTAAVGGRPRGALISQGNLLIAQSSLVDAWRLTEADVNLGMLPLFHVTGLGLMLTLQQAGGASVIAAKFDPAQAARDIEAHKVTVMAEFAPMLGNILDQAAPAQLASLRAVTGLDTPETIERFEATCPNATFWATFGQSETSGLSTFAPYRDRPKSAGRPLFWRTVAVVDAEDRPLPPGEVGEIVLRGPTVFKGYWNNAAATQHAFRNGWHHTGDMGRFDADGYLFYAGRA 398
               SCOP domains d3ivra_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhheeeeee...hhhhhhhhhhhh....eeee........ee.hhh...............eeeeeeee.--..eeeeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhh.eeee....hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeeeeehhhheeeeeee.hhh.....ee....eeeee............eeeeee......ee..hhhhhhhhhhhhheeeeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ivr A   3 SLHDFTLADVYRRNAALFPDRTAFMVDGVRLTHRDYLARAERLASGLLRDGVHTGDRVAILSQNCSEMIELIGAVALIGAILLPVNYRLNADEIAFVLGDGAPSVVVAGTDYRDIVAGVLPSLGGVKKAYAIGDGSGPFAPFKDLASDTPFSAPEFGAADGFVIIHTAA--GRPRGALISQGNLLIAQSSLVDAWRLTEADVNLGMLPLFHVTGLGLMLTLQQAGGASVIAAKFDPAQAARDIEAHKVTVMAEFAPMLGNILDQAAPAQLASLRAVTGLDTPETIERFEATCPNATFWATFGQSETSGLSTFAPYRDRPKSAGRPLFWRTVAVVDAEDRPLPPGEVGEIVLRGPTVFKGYWNNAAATQHAFRNGWHHTGDMGRFDADGYLFYAGRA 398
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        |- |     182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392      
                                                                                                                                                                                                  171  |                                                                                                                                                                                                                                
                                                                                                                                                                                                     174                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:393
 aligned with Q6NAE3_RHOPA | Q6NAE3 from UniProtKB/TrEMBL  Length:503

    Alignment length:395
                                    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     
         Q6NAE3_RHOPA     3 ALHDFTLADVYRRNAALFPDRTAFMVDGVRLTHRDYLARAERLASGLLRDGVHTGDRVAILSQNCSEMIELIGAVALIGAILLPVNYRLNADEIAFVLGDGAPSVVVAGTDYRDIVAGVLPSLGGVKKAYAIGDGSGPFAPFKDLASDTPFSAPEFGAADGFVIIHTAAVGGRPRGALISQGNLLIAQSSLVDAWRLTEADVNLGMLPLFHVTGLGLMLTLQQAGGASVIAAKFDPAQAARDIEAHKVTVMAEFAPMLGNILDQAAPAQLASLRAVTGLDTPETIERFEATCPNATFWATFGQSETSGLSTFAPYRDRPKSAGRPLFWRTVAVVDAEDRPLPPGEVGEIVLRGPTVFKGYWNNAAATQHAFRNGWHHTGDMGRFDADGYLFYAGR 397
               SCOP domains d3ivrb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh..eeee...hhhhhhhhhhhh....eeee........ee.hhhh..............eeeeeeee.--..eeeeeeehhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeeeeeehhhheeeeeee.hhh.....ee....eeeee............eeeeee......ee..hhhhhhhhhhhhheeeeeeeee.....eee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ivr B   3 SLHDFTLADVYRRNAALFPDRTAFMVDGVRLTHRDYLARAERLASGLLRDGVHTGDRVAILSQNCSEMIELIGAVALIGAILLPVNYRLNADEIAFVLGDGAPSVVVAGTDYRDIVAGVLPSLGGVKKAYAIGDGSGPFAPFKDLASDTPFSAPEFGAADGFVIIHTAA--GRPRGALISQGNLLIAQSSLVDAWRLTEADVNLGMLPLFHVTGLGLMLTLQQAGGASVIAAKFDPAQAARDIEAHKVTVMAEFAPMLGNILDQAAPAQLASLRAVTGLDTPETIERFEATCPNATFWATFGQSETSGLSTFAPYRDRPKSAGRPLFWRTVAVVDAEDRPLPPGEVGEIVLRGPTVFKGYWNNAAATQHAFRNGWHHTGDMGRFDADGYLFYAGR 397
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162        |- |     182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392     
                                                                                                                                                                                                  171  |                                                                                                                                                                                                                               
                                                                                                                                                                                                     174
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IVR)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q6NAE3_RHOPA | Q6NAE3)
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:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0004467    long-chain fatty acid-CoA ligase activity    Catalysis of the reaction: ATP + a long-chain fatty acid + CoA = AMP + diphosphate + an acyl-CoA; a long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
biological process
    GO:0001676    long-chain fatty acid metabolic process    The chemical reactions and pathways involving long-chain fatty acids, A long-chain fatty acid is a fatty acid with a chain length between C13 and C22.
    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.

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