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(-) Description

Title :  MALONYL-COA LIGASE TERNARY PRODUCT COMPLEX WITH MALONYL-COA AND AMP BOUND
 
Authors :  A. J. Hughes, A. T. Keatinge-Clay
Date :  15 Jul 10  (Deposition) - 30 Mar 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  A/B Topology Ababa Sandwich Beta-Barrel, Adenylate-Forming Enzyme Fold, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Hughes, A. Keatinge-Clay
Enzymatic Extender Unit Generation For In Vitro Polyketide Synthase Reactions: Structural And Functional Showcasing Of Streptomyces Coelicolor Matb.
Chem. Biol. V. 18 165 2011
PubMed-ID: 21338915  |  Reference-DOI: 10.1016/J.CHEMBIOL.2010.12.014

(-) Compounds

Molecule 1 - MALONYL-COA LIGASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MATB, SCC24.15, SCO2444
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 1902

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2MG1Ligand/IonMAGNESIUM ION
3MLC1Ligand/IonMALONYL-COENZYME A
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MLC1Ligand/IonMALONYL-COENZYME A
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MG-1Ligand/IonMAGNESIUM ION
3MLC2Ligand/IonMALONYL-COENZYME A

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:184 , VAL A:188 , HIS A:189 , ARG A:236 , SER A:261 , ARG A:283 , GLY A:285 , MET A:291 , LYS A:390 , GLY A:392 , GLY A:393 , TYR A:394 , ARG A:461 , AMP A:487 , HOH A:503 , HOH A:638 , HOH A:666 , HOH A:705 , HOH A:710BINDING SITE FOR RESIDUE MLC A 486
2AC2SOFTWARESER A:261 , ALA A:262 , ALA A:263 , GLU A:282 , ARG A:283 , GLY A:285 , MET A:286 , THR A:287 , VAL A:306 , ASP A:368 , LYS A:390 , LYS A:395 , MLC A:486 , HOH A:604 , HOH A:657 , HOH A:690 , HOH A:749 , HOH A:750BINDING SITE FOR RESIDUE AMP A 487
3AC3SOFTWAREHOH A:731 , HOH A:732 , HOH A:733 , HOH A:734 , HOH A:735 , HOH A:736BINDING SITE FOR RESIDUE MG A 499

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ser A:9 -Pro A:10

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NYR)

(-) 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:460
 aligned with Q9L0A2_STRCO | Q9L0A2 from UniProtKB/TrEMBL  Length:485

    Alignment length:468
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463        
         Q9L0A2_STRCO     4 LFPALSPAPTGAPADRPALRFGERSLTYAELAAAAGATAGRIGGAGRVAVWATPAMETGVAVVAALLAGVAAVPLNPKSGDKELAHILSDSAPSLVLAPPDAELPPALGALERVDVDVRARGAVPEDGADDGDPALVVYTSGTTGPPKGAVIPRRALATTLDALADAWQWTGEDVLVQGLPLFHVHGLVLGILGPLRRGGSVRHLGRFSTEGAARELNDGATMLFGVPTMYHRIAETLPADPELAKALAGARLLVSGSAALPVHDHERIAAATGRRVIERYGMTETLMNTSVRADGEPRAGTVGVPLPGVELRLVEEDGTPIAALDGESVGEIQVRGPNLFTEYLNRPDATAAAFTEDGFFRTGDMAVRDPDGYVRIVGRKATDLIKSGGYKIGAGEIENALLEHPEVREAAVTGEPDPDLGERIVAWIVPADPAAPPALGTLADHVAARLAPHKRPRVVRYLDAVPR 471
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------AMP-binding-3nyrA   01 A:30-416                                                                                                                                                                                                                                                                                                                                                                    ------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.eeeee..eeeehhhhhhhhhhhhhh..---.eeee...hhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhh..eeee......hhhhh..eeee..................eeeeeee.......eeeeeehhhhhhhhhhhhhhhh.....eeee.....hhhhhh..hhhhhhhh.eeee....hhhhhhhhhh....eeeehhhhhhhhhhhh..hhhhhhhhhhh.eeee.....hhhhhhhhhhhhh...eeeeeehhheeeee.............ee....eeeee-----..........eeeeee......ee..hhhhhhhh......eeeeeeeee.....eeeeee.....eee..eeehhhhhhhhhh....eeeeeeeeeee...eeeeeeeeee.......hhhhhhhhhhhhhhhhhh..eeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3nyr A   4 LFPALSPAPTGAPADRPALRFGERSLTYAELAAAAGATAGRIG---RVAVWATPAMETGVAVVAALLAGVAAVPLNPKSGDKELAHILSDSAPSLVLAPPDAELPPALGALERVDVDVRARGAVPEDGADDGDPALVVYTSGTTGPPKGAVIPRRALATTLDALADAWQWTGEDVLVQGLPLFHVHGLVLGILGPLRRGGSVRHLGRFSTEGAARELNDGATMLFGVPTMYHRIAETLPADPELAKALAGARLLVSGSAALPVHDHERIAAATGRRVIERYGMTETLMNTSVRADGEPRAGTVGVPLPGVELRLV-----PIAALDGESVGEIQVRGPNLFTEYLNRPDATAAAFTEDGFFRTGDMAVRDPDGYVRIVGRKATDLIKSGGYKIGAGEIENALLEHPEVREAAVTGEPDPDLGERIVAWIVPADPAAPPALGTLADHVAARLAPHKRPRVVRYLDAVPR 471
                                    13        23        33        43  |   | 53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313    |    -|      333       343       353       363       373       383       393       403       413       423       433       443       453       463        
                                                                     46  50                                                                                                                                                                                                                                                                         318   324
   Legend:   → Mismatch (orange background)
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  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 3NYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: ANL (32)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9L0A2_STRCO | Q9L0A2)
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: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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  3nyr
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 Related Entries

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

UniProtKB/TrEMBL
        Q9L0A2_STRCO | Q9L0A2: 3nyq

(-) Related Entries Specified in the PDB File

1pg3 1ry2 1t5d 2d1r 3e7w 3ite 3nyq