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(-) Description

Title :  CRYSTAL STRUCTURE OF CYTIDINE MONOPHOSPHATE HYDROXYMETHYLASE MILA WITH DCMP
 
Authors :  G. Zhao, X. He
Date :  03 May 16  (Deposition) - 15 Mar 17  (Release) - 15 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cmp Hydroxymethylase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Zhao, C. Chen, W. Xiong, T. Gao, Z. Deng, G. Wu, X. He
Structural Basis Of The Substrate Preference Towards Cmp Fo A Thymidylate Synthase Mila Involved In Mildiomycin Biosynthesis
Sci Rep V. 6 39675 2016
PubMed-ID: 28000775  |  Reference-DOI: 10.1038/SREP39675

(-) Compounds

Molecule 1 - CMP 5-HYDROXYMETHYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 5-329
    Gene: MILA
    Organism Scientific: STREPTOMYCES RIMOFACIENS
    Organism Taxid: 504097
    Synonym: CYTIDINE MONOPHOSPHATE HYDROXYMETHYLASE MILA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DCM2Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:31 , TYR A:104 , CYS A:155 , ARG A:175 , ALA A:176 , ASN A:177 , ASP A:178 , ASP A:186 , HIS A:216 , TYR A:218 , HOH A:526 , HOH A:536 , HOH A:537 , LYS B:133 , ARG B:134 , HOH B:633binding site for residue DCM A 401
2AC2SOFTWARELYS A:133 , ARG A:134 , HOH A:602 , ARG B:31 , TYR B:104 , CYS B:155 , ARG B:175 , ALA B:176 , ASN B:177 , ASP B:178 , ASP B:186 , HIS B:216 , TYR B:218 , HOH B:530 , HOH B:542 , HOH B:552binding site for residue DCM B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JP9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5JP9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JP9)

(-) Exons   (0, 0)

(no "Exon" information available for 5JP9)

(-) 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:317
                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..eeehhhhh.eeeeeeeeeee.........hhhhh.hhhhhhhhhhhhhh...hhhhhhh.hhhhhhhh.........hhhhhhhh......hhhhhhhhhhhhh......eee..hhhhhh.........eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jp9 A   5 TFGTFQDAYLSQLRDIYHSPEFRNAPRGQASRERIGAGFRLLDPVQRHISVPARRANVVFNFAEALWYLSGSDRLDFIQYYAPGIAAYSADGRTLRGTAYGPRIFRHPAGGVNQWENVVKTLTDDPDSKRAVIQIFDPRELAVADNIDVACTLALQFLIRDGLLCGIGYMRANDAFRGAVSDVFSFTFLQEFTARYLGLGIGTYHHVVGSVHIYDSDARWAERVLDAPGFPAMPDGDNWPHVRRVLEWEERLRTNAARLSADALDALDLPAYWKHVVALFEAHRQVRHEDTPDRALLAALPEVYRQSLAVKWPGHFG 329
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224      |242       252       262       272       282       292       302       312       322       
                                                                                                                                                                                                                                                            231|                                                                                         
                                                                                                                                                                                                                                                             240                                                                                         


Chain B from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..eeehhhhh.eeeeeeeeeee.........hhhhh.hhhhhhhhhhhhhh...hhhhhhh.hhhhhhhh.........hhhhhhhh......hhhhhhhhhhhhh......eee....hhhhh........eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.....hhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5jp9 B   5 TFGTFQDAYLSQLRDIYHSPEFRNAPRGQASRERIGAGFRLLDPVQRHISVPARRANVVFNFAEALWYLSGSDRLDFIQYYAPGIAAYSADGRTLRGTAYGPRIFRHPAGGVNQWENVVKTLTDDPDSKRAVIQIFDPRELAVADNIDVACTLALQFLIRDGLLCGIGYMRANDAFRGAVSDVFSFTFLQEFTARYLGLGIGTYHHVVGSVHIYDSDARWAERVLDARPGFPAMPDGDNWPHVRRVLEWEERLRTNAARLSADALDALDLPAYWKHVVALFEAHRQVRHEDTPDRALLAALPEVYRQSLAVKWPGHFG 329
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224      |241       251       261       271       281       291       301       311       321        
                                                                                                                                                                                                                                                            231|                                                                                          
                                                                                                                                                                                                                                                             239
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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 5JP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JP9)

(-) Gene Ontology  (3, 3)

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 Related Entries

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

UniProtKB/TrEMBL
        B4Y380_9ACTN | B4Y380: 5b6d 5b6e 5jnh

(-) Related Entries Specified in the PDB File

5jnh