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(-) Description

Title :  CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE IN COMPLEX WITH THE CIS ISOMER OF AMICLENOMYCIN
 
Authors :  J. Sandmark, S. Mann, A. Marquet, G. Schneider
Date :  02 Sep 02  (Deposition) - 04 Dec 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Aminotransferase, Fold Type I, Subclass Ii, Amiclenomycin, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sandmark, S. Mann, A. Marquet, G. Schneider
Structural Basis For The Inhibition Of The Biosynthesis Of Biotin By The Antibiotic Amiclenomycin
J. Biol. Chem. V. 277 43352 2002
PubMed-ID: 12218056  |  Reference-DOI: 10.1074/JBC.M207239200

(-) Compounds

Molecule 1 - 7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BIOA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE, DAPA AMINOTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACZ2Ligand/IonCIS-AMICLENOMYCIN
2NA2Ligand/IonSODIUM ION
3PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:52 , TRP A:53 , TYR A:144 , LYS A:274 , ARG A:391 , PHE A:393 , PLP A:730 , HOH A:749 , HOH A:767 , HOH A:806 , HOH B:976BINDING SITE FOR RESIDUE ACZ A 731
2AC2SOFTWARETHR A:309 , TRP B:52 , TYR B:144 , ALA B:217 , ARG B:391 , PHE B:393 , TYR B:398 , PLP B:830 , HOH B:900 , HOH B:914 , HOH B:919 , HOH B:973 , HOH B:992BINDING SITE FOR RESIDUE ACZ B 831
3AC3SOFTWAREVAL B:96 , THR B:99 , PRO B:100 , LEU B:103 , HOH B:880BINDING SITE FOR RESIDUE NA B 701
4AC4SOFTWAREVAL A:96 , THR A:99 , PRO A:100 , LEU A:103 , HOH A:774BINDING SITE FOR RESIDUE NA A 702
5AC5SOFTWAREGLY A:112 , SER A:113 , TYR A:144 , HIS A:145 , GLY A:146 , GLU A:211 , ASP A:245 , ILE A:247 , LYS A:274 , ACZ A:731 , HOH A:744 , HOH A:794 , HOH A:797 , PRO B:308 , THR B:309 , HOH B:832 , HOH B:847BINDING SITE FOR RESIDUE PLP A 730
6AC6SOFTWAREPRO A:308 , THR A:309 , HOH A:735 , TRP B:53 , GLY B:112 , SER B:113 , HIS B:145 , GLU B:211 , ASP B:245 , ILE B:247 , ALA B:248 , LYS B:274 , ACZ B:831 , HOH B:836 , HOH B:862 , HOH B:875BINDING SITE FOR RESIDUE PLP B 830

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MLY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1MLY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MLY)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.BIOA_ECOLI242-279
 		  2A:242-279
B:242-279

(-) Exons   (0, 0)

(no "Exon" information available for 1MLY)

(-) 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:427
 aligned with BIOA_ECOLI | P12995 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
           BIOA_ECOLI     1 MTTDDLAFDQRHIWHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGKALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
               SCOP domains d1mlya_ A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1mlyA01 A:1-60,A:331-427                                    1mlyA02 A:61-330 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                          1mlyA01 A:1-60,A:331-427 Aspartate Aminotransferase, domain 1                                    - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.............eeeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhh.......hhhhhh......eee.......-...hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:242-279   ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mly A   1 MTTDDLAFDQRHILHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRM-GEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGKALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 | |   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
                                                                                                                                                                                                               182 |                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                 184                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:428
 aligned with BIOA_ECOLI | P12995 from UniProtKB/Swiss-Prot  Length:429

    Alignment length:428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420        
           BIOA_ECOLI     1 MTTDDLAFDQRHIWHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGKALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
               SCOP domains d1mlyb_ B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase, BioA                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1mlyB01 B:1-60,B:331-428                                    1mlyB02 B:61-330 Type I PLP-dependent aspartate aminotransferase-like (Major domain)                                                                                                                                                                                          1mlyB01 B:1-60,B:331-428 Aspartate Aminotransferase, domain 1                                      CATH domains
           Pfam domains (1) ---------------------------Aminotran_3-1mlyB01 B:28-372                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------------------Aminotran_3-1mlyB02 B:28-372                                                                                                                                                                                                                                                                                                                             -------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh.............eeeeeee..eeee....eeee.............hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhh.......hhhhhh......eee...........hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhhh.....eeeeeehhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: B:242-279   ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mly B   1 MTTDDLAFDQRHILHPYTSMTSPLPVYPVVSAEGCELILSDGRRLVDGMSSWWAAIHGYNHPQLNAAMKSQIDAMSHVMFGGITHAPAIELCRKLVAMTPQPLECVFLADSGSVAVEVAMKMALQYWQAKGEARQRFLTFRNGYHGDTFGAMSVCDPDNSMHSLWKGYLPENLFAPAPQSRMDGEWDERDMVGFARLMAAHRHEIAAVIIEPIVQGAGGMRMYHPEWLKRIRKICDREGILLIADEIATGFGRTGKLFACEHAEIAPDILCLGKALTGGTMTLSATLTTREVAETISNGEAGCFMHGPTFMGNPLACAAANASLAILESGDWQQQVADIEVQLREQLAPARDAEMVADVRVLGAIGVVETTHPVNMAALQKFFVEQGVWIRPFGKLIYLMPPYIILPQQLQRLTAAVNRAVQDETFFC 428
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BIOA_ECOLI | P12995)
molecular function
    GO:0004015    adenosylmethionine-8-amino-7-oxononanoate transaminase activity    Catalysis of the reaction: 8-amino-7-oxononanoate + S-adenosyl-L-methionine(1+) = 7,8-diaminononanoate + S-adenosyl-4-methylthio-2-oxobutanoate.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    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.
biological process
    GO:0009102    biotin biosynthetic process    The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
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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  1mly
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  2.6.1.62
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 Related Entries

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

UniProtKB/Swiss-Prot
        BIOA_ECOLI | P12995: 1dty 1mgv 1mlz 1qj3 1qj5 1s06 1s07 1s08 1s09 1s0a

(-) Related Entries Specified in the PDB File

1dty WT STRUCTURE OF THE SAME ENZYME
1mgv R391A MUTANT OF THE SAME ENZYME
1mlz 1MLZ CONTAINS THE SAME ENZYME COMPLEXED WITH THE TRANS- ISOMER OF AMICLENOMYCIN
1qj3 STRUCTURE OF THE SUBSTRATE COMPLEX WITH THE WT ENZYME
1qj5 WT STRUCTURE OF THE SAME ENZYME