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(-) Description

Title :  CRYSTAL STRUCTURES AND ENZYMATIC MECHANISMS OF A POPULUS TOMENTOSA 4-COUMARATE:COA LIGASE
 
Authors :  Y. Hu, L. Yin, Y. Gai, X. X. Wang, D. C. Wang
Date :  14 Jun 10  (Deposition) - 08 Sep 10  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  4-Coumarate:Coa Ligase, 4Cl, Phenylpropanoid Biosynthesis, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Hu, Y. Gai, L. Yin, X. Wang, C. Feng, L. Feng, D. Li, X. N. Jiang, D. C. Wang
Crystal Structures Of A Populus Tomentosa 4-Coumarate:Coa Ligase Shed Light On Its Enzymatic Mechanisms
Plant Cell V. 22 3093 2010
PubMed-ID: 20841425  |  Reference-DOI: 10.1105/TPC.109.072652

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 6.2.1.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE31
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: POPULUS TOMENTOSA
    Organism Taxid: 118781

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1AYL1Ligand/Ion5'-O-{(S)-HYDROXY[3-(4-HYDROXYPHENYL)PROPOXY]PHOSPHORYL}ADENOSINE
2EPE3Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:236 , SER A:240 , LYS A:303 , GLY A:306 , ALA A:307 , PRO A:308 , GLN A:328 , GLY A:329 , GLY A:331 , THR A:333 , PRO A:337 , VAL A:338 , ASP A:417 , LYS A:434 , LYS A:438 , GLN A:443 , HOH A:571 , HOH A:583 , HOH A:655 , HOH A:869BINDING SITE FOR RESIDUE AYL A 537
2AC2SOFTWARELYS A:115 , ALA A:119 , TYR A:185 , PRO A:193 , LYS A:505 , HOH A:596 , HOH A:598 , HOH A:605 , HOH A:618 , HOH A:638 , HOH A:744 , HOH A:793 , HOH A:809BINDING SITE FOR RESIDUE EPE A 538
3AC3SOFTWAREASP A:15 , ILE A:16 , TYR A:17 , ILE A:18 , LYS A:20 , VAL A:76 , ILE A:100 , SER A:120 , ARG A:121 , ASN A:363 , LYS A:394 , HOH A:562 , HOH A:608 , HOH A:610 , HOH A:622 , HOH A:892BINDING SITE FOR RESIDUE EPE A 539
4AC4SOFTWAREGLU A:348 , PRO A:349 , PHE A:350 , ASP A:351 , HOH A:1036BINDING SITE FOR RESIDUE EPE A 540

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NI2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:336 -Pro A:337

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NI2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NI2)

(-) Exons   (0, 0)

(no "Exon" information available for 3NI2)

(-) 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:528
 aligned with Q941M3_POPTO | Q941M3 from UniProtKB/TrEMBL  Length:536

    Alignment length:528
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524        
         Q941M3_POPTO     5 EEFIFRSKLPDIYIPKNLPLHSYVLENLSNHSSKPCLINGANGDVYTYADVELTARRVASGLNKIGIQQGDVIMLFLPSSPEFVLAFLGASHRGAIITAANPFSTPAELAKHAKASRAKLLITQACYYEKVKDFARESDVKVMCVDSAPDGCLHFSELTQADENEAPQVDISPDDVVALPYSSGTTGLPKGVMLTHKGLITSVAQQVDGDNPNLYFHSEDVILCVLPMFHIYALNSIMLCGLRVGAPILIMPKFEIGSLLGLIEKYKVSIAPVVPPVMMSIAKSPDLDKHDLSSLRMIKSGGAPLGKELEDTVRAKFPQARLGQGYGMTEAGPVLAMCLAFAKEPFDIKPGACGTVVRNAEMKIVDPETGASLPRNQPGEICIRGDQIMKGYLNDPEATSRTIDKEGWLHTGDIGYIDDDDELFIVDRLKELIKYKGFQVAPAELEALLIAHPEISDAAVVGLKDEDAGEVPVAFVVKSEKSQATEDEIKQYISKQVIFYKRIKRVFFIEAIPKAPSGKILRKNLKEK 532
               SCOP domains d3ni2a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ----------------------------------------------AMP-binding-3ni2A01 A:51-464                                                                                                                                                                                                                                                                                                                                                                                                  ---------------------------------------DUF4009-3ni2A02 A:504-532     Pfam domains
         Sec.struct. author ..................hhhhhhh.hhhhh...eeeee.....eeehhhhhhhhhhhhhhhhhh......eeeee...hhhhhhhhhhhhhhh.eeee.....hhhhhhhhhhhhheeeeee.hhhhhhhhhhhh....eeee........eehhhhhh.hhhhh.........eee..ee.......eeeeeehhhhhhhhhhhhh.............eee.....hhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhh..eeeehhhhhhhhhh..hhhhh......eeeee....hhhhhhhhhhhh...eeeeeee.hhhh.eeee.hhhh............ee....eeeee.............eeeeee......ee..hhhhhhhhh.....eeeeeeeee.....eeeeee....eee..eeehhhhhhhhhhh...eeeeeeeeeee...eeeeeeeeee......hhhhhhhhhhh..hhhhh..eeee............hhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ni2 A   5 EEFIFRSKLPDIYIPKNLPLHSYVLENLSNHSSKPCLINGANGDVYTYADVELTARRVASGLNKIGIQQGDVIMLFLPSSPEFVLAFLGASHRGAIITAANPFSTPAELAKHAKASRAKLLITQACYYEKVKDFARESDVKVMCVDSAPDGCLHFSELTQADENEAPQVDISPDDVVALPYSSGTTGLPKGVMLTHKGLITSVAQQVDGDNPNLYFHSEDVILCVLPMFHIYALNSIMLCGLRVGAPILIMPKFEIGSLLGLIEKYKVSIAPVVPPVMMSIAKSPDLDKHDLSSLRMIKSGGAPLGKELEDTVRAKFPQARLGQGYGMTEAGPVLAMCLAFAKEPFDIKPGACGTVVRNAEMKIVDPETGASLPRNQPGEICIRGDQIMKGYLNDPEATSRTIDKEGWLHTGDIGYIDDDDELFIVDRLKELIKYKGFQVAPAELEALLIAHPEISDAAVVGLKDEDAGEVPVAFVVKSEKSQATEDEIKQYISKQVIFYKRIKRVFFIEAIPKAPSGKILRKNLKEK 532
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524
   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/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NI2)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: ANL (32)
(-)
Clan: no clan defined [family: DUF4009] (14)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q941M3_POPTO | Q941M3)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    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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  Cis Peptide Bonds
    Gly A:336 - Pro A:337   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q941M3_POPTO | Q941M3: 3a9u 3a9v

(-) Related Entries Specified in the PDB File

3a9u SAME PROTEIN, APO FORM
3a9v SAME PROTEIN, COMPLEXED WITH AMP