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(-) Description

Title :  CRYSTAL STRUCTURE OF ACLACINOMYCIN METHYLESTERASE (RDMC) WITH BOUND PRODUCT ANALOGUE, 10-DECARBOXYMETHYLACLACINOMYCIN A (DCMA)
 
Authors :  A. Jansson, J. Niemi, P. Mantsala, G. Schneider, Structural Proteomics In Europe (Spine)
Date :  18 Jul 03  (Deposition) - 25 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Anthracycline, Methylesterase, Hydrolase, Polyketide, Streptomyces, Tailoring Enzyme, Structural Proteomics In Europe, Spine, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Jansson, J. Niemi, P. Mantsala, G. Schneider
Crystal Structure Of Aclacinomycin Methylesterase With Bound Product Analogues: Implications For Anthracycline Recognition And Mechanism.
J. Biol. Chem. V. 278 39006 2003
PubMed-ID: 12878604  |  Reference-DOI: 10.1074/JBC.M304008200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ACLACINOMYCIN METHYLESTERASE
    Chains: A
    Engineered: YES
    Expression System: STREPTOMYCES LIVIDANS TK24
    Expression System Plasmid: PRDM*12
    Expression System Strain: TK24
    Expression System Taxid: 457428
    Expression System Vector Type: PIJ487
    Gene: RDMC
    Organism Scientific: STREPTOMYCES PURPURASCENS
    Organism Taxid: 1924
    Synonym: RDMC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2AKA1Ligand/Ion10-DECARBOXYMETHYLACLACINOMYCIN A (DCMAA)
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:102 , MET A:103 , THR A:106 , LEU A:126 , GLY A:128 , PHE A:134 , ASP A:135 , PHE A:158 , GLU A:197 , HIS A:219 , TYR A:220 , LEU A:222 , LEU A:224 , ILE A:250 , 1PE A:2712 , SO4 A:3482 , HOH A:3519 , HOH A:3729 , HOH A:3736BINDING SITE FOR RESIDUE AKA A 600
2AC2SOFTWAREGLY A:32 , MET A:165 , LYS A:182 , TRP A:183 , GLU A:215 , AKA A:600 , 1PE A:2712 , HOH A:3730 , HOH A:3734 , HOH A:3736BINDING SITE FOR RESIDUE SO4 A 3482
3AC3SOFTWARELEU A:34 , LEU A:37 , GLY A:38 , LEU A:101 , TRP A:183 , TYR A:198 , GLU A:202 , ALA A:205 , HIS A:276 , AKA A:600 , SO4 A:3482 , HOH A:3735 , HOH A:3736BINDING SITE FOR RESIDUE 1PE A 2712

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q0Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:253 -Pro A:254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q0Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Q0Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1Q0Z)

(-) 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:297
 aligned with RDMC_STREF | Q54528 from UniProtKB/Swiss-Prot  Length:298

    Alignment length:297
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       
           RDMC_STREF     2 SERIVPSGDVELWSDDFGDPADPALLLVMGGNLSALGWPDEFARRLADGGLHVIRYDHRDTGRSTTRDFAAHPYGFGELAADAVAVLDGWGVDRAHVVGLSMGATITQVIALDHHDRLSSLTMLLGGGLDIDFDANIERVMRGEPTLDGLPGPQQPFLDALALMNQPAEGRAAEVAKRVSKWRILSGTGVPFDDAEYARWEERAIDHAGGVLAEPYAHYSLTLPPPSRAAELREVTVPTLVIQAEHDPIAPAPHGKHLAGLIPTARLAEIPGMGHALPSSVHGPLAEVILAHTRSAA 298
               SCOP domains d1q0za_ A: Aclacinomycin methylesterase RdmC                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1q0zA00 A:2-298  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeeeee......eeeee.....hhhhhhhhhhhhhhh...eeeee...........hhhhh..hhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhh...........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhh...hhhhhhhhhhh...eeeeee........hhhhhhhh....eeeeee.......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q0z A   2 SERIVPSGDVELWSDDFGDPADPALLLVMGGNLSALGWPDEFARRLADGGLHVIRYDHRDTGRSTTRDFAAHPYGFGELAADAVAVLDGWGVDRAHVVGLSMGATITQVIALDHHDRLSSLTMLLGGGLDIDFDANIERVMRGEPTLDGLPGPQQPFLDALALMNQPAEGRAAEVAKRVSKWRILSGTGVPFDDAEYARWEERAIDHAGGVLAEPYAHYSLTLPPPSRAAELREVTVPTLVIQAEHDPIAPAPHGKHLAGLIPTARLAEIPGMGHALPSSVHGPLAEVILAHTRSAA 298
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q0Z)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RDMC_STREF | Q54528)
molecular function
    GO:0052689    carboxylic ester hydrolase activity    Catalysis of the hydrolysis of a carboxylic ester bond.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.

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  1q0z
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 Related Entries

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

UniProtKB/Swiss-Prot
        RDMC_STREF | Q54528: 1q0r

(-) Related Entries Specified in the PDB File

1q0r CRYSTAL STRUCTURE OF RDMC IN COMPLEX WITH DCMAT
st_1