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(-) Description

Title :  CRYSTAL STRUCTURE OF CHMJ, A 3'-MONOEPIMERASE APOENZYME FROM STREPTOMYCES BIKINIENSIS
 
Authors :  H. M. Holden, R. L. Kubiak
Date :  18 Oct 12  (Deposition) - 21 Nov 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  3'-Monoepimerase, Natural Product, Deoxysugar, Chalcomycin, Dtdp- Mycinose, Cupin Fold, Nucleotide-Linked Sugar, Epimerization, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Kubiak, R. K. Phillips, M. W. Zmudka, M. R. Ahn, E. M. Maka, G. L. Pyeatt, S. J. Roggensack, H. M. Holden
Structural And Functional Studies On A 3'-Epimerase Involve In The Biosynthesis Of Dtdp-6-Deoxy-D-Allose.
Biochemistry V. 51 9375 2012
PubMed-ID: 23116432  |  Reference-DOI: 10.1021/BI3012737

(-) Compounds

Molecule 1 - PUTATIVE 3-EPIMERASE IN D-ALLOSE PATHWAY
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-31B(+)
    Expression System Strain: ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CHMJ
    Organism Scientific: STREPTOMYCES BIKINIENSIS
    Organism Taxid: 1896

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:17 , ASP A:19 , ARG A:21 , GLY A:22 , SER A:24 , ARG B:57BINDING SITE FOR RESIDUE EDO A 201
02AC2SOFTWAREPHE A:28 , ARG A:29 , SER A:32 , TYR A:71 , HOH A:333BINDING SITE FOR RESIDUE EDO A 202
03AC3SOFTWAREASN A:47 , LYS A:70 , TYR A:130BINDING SITE FOR RESIDUE EDO A 203
04AC4SOFTWAREARG A:95BINDING SITE FOR RESIDUE EDO A 204
05AC5SOFTWAREARG A:57 , ARG B:21BINDING SITE FOR RESIDUE CL A 205
06AC6SOFTWAREARG A:57 , HIS B:17 , ASP B:19 , ARG B:21 , GLY B:22 , SER B:24BINDING SITE FOR RESIDUE EDO B 201
07AC7SOFTWAREGLN B:12 , PHE B:28 , ARG B:29 , SER B:32 , TYR B:71 , HOH B:329BINDING SITE FOR RESIDUE EDO B 202
08AC8SOFTWAREASN B:47 , LYS B:70 , TYR B:130BINDING SITE FOR RESIDUE EDO B 203
09AC9SOFTWARESER B:5 , GLU B:7 , HOH B:331BINDING SITE FOR RESIDUE EDO B 204
10BC1SOFTWAREMET B:1 , TRP B:10 , ALA B:36BINDING SITE FOR RESIDUE EDO B 205
11BC2SOFTWAREARG A:21 , ARG B:57BINDING SITE FOR RESIDUE CL B 206
12BC3SOFTWAREHIS C:17 , ASP C:19 , ARG C:21 , GLY C:22 , SER C:24 , ARG D:57BINDING SITE FOR RESIDUE EDO C 201
13BC4SOFTWAREARG C:57 , HIS C:60 , ARG D:21BINDING SITE FOR RESIDUE CL C 202
14BC5SOFTWAREARG C:21 , ARG D:57 , HIS D:60BINDING SITE FOR RESIDUE CL C 203
15BC6SOFTWAREARG C:57 , HIS D:17 , ASP D:19 , ARG D:21 , GLY D:22 , ARG D:23 , SER D:24BINDING SITE FOR RESIDUE EDO D 201
16BC7SOFTWAREGLN D:12 , PHE D:28 , ARG D:29 , TYR D:71BINDING SITE FOR RESIDUE EDO D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HN0)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:58 -Ile A:59
2Ile A:64 -Pro A:65
3Pro A:65 -Pro A:66
4Gly B:58 -Ile B:59
5Ile B:64 -Pro B:65
6Pro B:65 -Pro B:66
7Gly C:58 -Ile C:59
8Ile C:64 -Pro C:65
9Pro C:65 -Pro C:66
10Gly D:58 -Ile D:59
11Ile D:64 -Pro D:65
12Pro D:65 -Pro D:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HN0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HN0)

(-) Exons   (0, 0)

(no "Exon" information available for 4HN0)

(-) 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:198
                                                                                                                                                                                                                                      
               SCOP domains d4hn0a_ A: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....eeee...eeee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee........eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hn0 A   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGIHYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVYLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLE 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4hn0b_ B: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....eeee....eee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee........eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hn0 B   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGIHYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVYLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLE 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        


Chain C from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4hn0c_ C: automated matches                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee.....eeee...eeee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee....eeeeeee....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hn0 C   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGIHYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVYLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLE 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        


Chain D from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains d4hn0d_ D: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee....eee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee....eeeeeee....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hn0 D   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGIHYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVYLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRL 197
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HN0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HN0)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:58 - Ile A:59   [ RasMol ]  
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    Gly C:58 - Ile C:59   [ RasMol ]  
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    Ile A:64 - Pro A:65   [ RasMol ]  
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    Ile D:64 - Pro D:65   [ RasMol ]  
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  4hn0
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHMJ_STRBI | Q5SFD1: 4hmz 4hn1

(-) Related Entries Specified in the PDB File

4hmz CRYSTAL STRUCTURE OF CHMJ, A 3'-MONOEPIMERASE FROM STREPTOMYCES BIKINIENSIS IN COMPLEX WITH DTDP-QUINOVOSE
4hn1