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(-) Description

Title :  COMPLEX STRUCTURE OF VINN WITH 3-METHYLASPARTATE
 
Authors :  A. Miyanaga, J. Cieslak, Y. Shinohara, F. Kudo, T. Eguchi
Date :  15 May 14  (Deposition) - 01 Oct 14  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Five-Layered Alpha-Beta-Alpha-Beta-Alpha Sandwich Fold, Ligase, Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Miyanaga, J. Cieslak, Y. Shinohara, F. Kudo, T. Eguchi
The Crystal Structure Of The Adenylation Enzyme Vinn Reveal A Unique Beta-Amino Acid Recognition Mechanism
J. Biol. Chem. V. 289 31448 2014
PubMed-ID: 25246523  |  Reference-DOI: 10.1074/JBC.M114.602326

(-) Compounds

Molecule 1 - NON-RIBOSOMAL PEPTIDE SYNTHETASE
    Chains: A, B
    EC Number: 6.2.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD I
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN, UNP RESIDUES 1-379
    Gene: VINN
    Organism Scientific: STREPTOMYCES HALSTEDII
    Organism Taxid: 1944
    Strain: HC34

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
12AS2Ligand/Ion(2S,3S)-3-METHYL-ASPARTIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
12AS1Ligand/Ion(2S,3S)-3-METHYL-ASPARTIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
12AS1Ligand/Ion(2S,3S)-3-METHYL-ASPARTIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:230 , SER A:299 , ALA A:300 , GLY A:325 , GLN A:326 , THR A:327 , LYS A:330 , ARG A:331 , HOH A:770 , HOH A:776BINDING SITE FOR RESIDUE 2AS A 601
2AC2SOFTWARETRP B:229 , ASP B:230 , SER B:299 , ALA B:300 , GLY B:325 , GLN B:326 , THR B:327 , LYS B:330 , ARG B:331BINDING SITE FOR RESIDUE 2AS B 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WV5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WV5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WV5)

(-) Exons   (0, 0)

(no "Exon" information available for 3WV5)

(-) 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:387
 aligned with Q76KY2_STRHA | Q76KY2 from UniProtKB/TrEMBL  Length:478

    Alignment length:403
                                                     1                                                                                                                                                                                                                                                                                                                                                                                         
                                     -         -     |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375   
         Q76KY2_STRHA     - -------------------------MEDAFGTWTYQELLNHSQAFSAWLDGKGVARGERIVVQLPNIRQTVAVFYGACRRGVVFVPLNPGMKPFHLRSVIADADPRLVIAEDETAADRLRDVTDLPVYSIDSLWADVERLRDAGAGAEAVEVSPEDLAVLIYTSGSTAAPKAVACPHQQIVFAASSINAVLGYHAEDIVFCRMSVSWDFGLYKVLISTLTGAKLVLAGGEPDIALVKSLRESGATMMPIVPSLASMLTTLIRRDPEGAPTLRMFTNSAAALPQVTIDALRSAFPGAQVVRMYGQTECKRISIMPPHLEHERPDSVGLPLPGTTIEILDEDGTLLPPGEPGEITVTGPHVMAGYWRAPEITARAYRRDETTGAMRLHTGDYGHLDEDGFLYFGG 378
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh...eeee....eeehhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh..eeee.hhhhhhhhhhhh...eeehhhhhhhhhhhhhh.............eeeeee.........eeeeehhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh.eeee.----..hhhhhhhhhh..eeeehhhhhhhhhhhhhh.........eeee.....hhhhhhhhhhhh...eeeeee.hhhhh..ee.hhhhh........ee....eeee.----........eeeeee..........hhhhhhhhh--------..eeeeeeeee.....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wv5 A  23 KDLRYGGLVHDLLADSGKATPNSDAMEDAFGTWTYQELLNHSQAFSAWLDGKGVARGERIVVQLPNIRQTVAVFYGACRRGVVFVPLNPGMKPFHLRSVIADADPRLVIAEDETAADRLRDVTDLPVYSIDSLWADVERLRDAGAGAEAVEVSPEDLAVLIYTSGSTAAPKAVACPHQQIVFAASSINAVLGYHAEDIVFCRMSVSWDFGLYKVLISTLTGAKLVLA----DIALVKSLRESGATMMPIVPSLASMLTTLIRRDPEGAPTLRMFTNSAAALPQVTIDALRSAFPGAQVVRMYGQTECKRISIMPPHLEHERPDSVGLPLPGTTIEIL----TLLPPGEPGEITVTGPHVMAGYWRAPEITARAY--------MRLHTGDYGHLDEDGFLYFGG 425
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242      |  - |     262       272       282       292       302       312       322       332       342       352      |  - |     372       382       392   |     -  |    412       422   
                                                                                                                                                                                                                                                            249  254                                                                                                      359  364                             396      405                    


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with Q76KY2_STRHA | Q76KY2 from UniProtKB/TrEMBL  Length:478

    Alignment length:400
                                                    1                                                                                                                                                                                                                                                                                                                                                                                       
                                     -         -    |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376
         Q76KY2_STRHA     - ------------------------MEDAFGTWTYQELLNHSQAFSAWLDGKGVARGERIVVQLPNIRQTVAVFYGACRRGVVFVPLNPGMKPFHLRSVIADADPRLVIAEDETAADRLRDVTDLPVYSIDSLWADVERLRDAGAGAEAVEVSPEDLAVLIYTSGSTAAPKAVACPHQQIVFAASSINAVLGYHAEDIVFCRMSVSWDFGLYKVLISTLTGAKLVLAGGEPDIALVKSLRESGATMMPIVPSLASMLTTLIRRDPEGAPTLRMFTNSAAALPQVTIDALRSAFPGAQVVRMYGQTECKRISIMPPHLEHERPDSVGLPLPGTTIEILDEDGTLLPPGEPGEITVTGPHVMAGYWRAPEITARAYRRDETTGAMRLHTGDYGHLDEDGFLYF 376
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh...eeeee..eeeehhhhhhhhhhhhhhhhhh......eeee....hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhh..eeee.hhhhhhhhhhhh...eeehhhhhhhhhhhhhh.............eeeeee.........eeeeehhhhhhhhhhhhhhhh.....eeee.....hhhhhhhhhhhhhhh.eeee..-------.hhhhhhh..eeeehhhhhhhhhh----------...eeee.....hhhhhhhhhhhh...eeeeee.hhhhh..ee.hhhhh........ee....eee.-------------.eeeee..........hhhhhhhhh--------..eeeeee....---.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wv5 B  24 DLRYGGLVHDLLADSGKATPNSDAMEDAFGTWTYQELLNHSQAFSAWLDGKGVARGERIVVQLPNIRQTVAVFYGACRRGVVFVPLNPGMKPFHLRSVIADADPRLVIAEDETAADRLRDVTDLPVYSIDSLWADVERLRDAGAGAEAVEVSPEDLAVLIYTSGSTAAPKAVACPHQQIVFAASSINAVLGYHAEDIVFCRMSVSWDFGLYKVLISTLTGAKLVLAG-------VKSLRESGATMMPIVPSLASMLTT----------TLRMFTNSAAALPQVTIDALRSAFPGAQVVRMYGQTECKRISIMPPHLEHERPDSVGLPLPGTTIEI-------------GEITVTGPHVMAGYWRAPEITARAY--------MRLHTGDYGHLD---FLYF 423
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      |  -    |  263       273       | -       293       303       313       323       333       343       353    |    -       373       383       393  |      - |     413  |   |423
                                                                                                                                                                                                                                                            250     258                    281        292                                                               358           372                     396      405        416 420
   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 3WV5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WV5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WV5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q76KY2_STRHA | Q76KY2)
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.
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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 Related Entries

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

UniProtKB/TrEMBL
        Q76KY2_STRHA | Q76KY2: 3wv4 3wvn

(-) Related Entries Specified in the PDB File

3wv4