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(-) Description

Title :  CRYSTAL STRUCTURE OF CHMJ, A 3'-MONOEPIMERASE FROM STREPTOMYCES BIKINIENSIS IN COMPLEX WITH DTDP-QUINOVOSE
 
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 :  2.00
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, Dtdp-Quinovose, 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, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
118T4Ligand/Ion[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL DIHYDROGEN DIPHOSPHATE
2EDO7Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
118T2Ligand/Ion[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL DIHYDROGEN DIPHOSPHATE
2EDO3Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
118T2Ligand/Ion[(2R,3S,5R)-3-HYDROXY-5-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)TETRAHYDROFURAN-2-YL]METHYL(2R,3R,4S,5S,6R)-3,4,5-TRIHYDROXY-6-METHYLTETRAHYDRO-2H-PYRAN-2-YL DIHYDROGEN DIPHOSPHATE
2EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:28 , ARG A:29 , SER A:32 , TYR A:71 , HOH A:401BINDING SITE FOR RESIDUE EDO A 301
02AC2SOFTWARETHR A:62 , GLN A:68 , TYR A:136 , ALA A:137 , PRO A:138 , GLU A:141 , HOH A:468BINDING SITE FOR RESIDUE EDO A 302
03AC3SOFTWAREGLN A:45 , ASN A:47 , ARG A:57 , HIS A:60 , LYS A:70 , ARG A:117 , LEU A:128 , TYR A:130 , TYR A:136 , GLU A:141 , ARG A:166 , HOH A:444 , HOH A:448 , HOH A:451 , HOH A:453 , HOH A:466 , HOH A:506 , HOH A:513 , HIS B:17 , ARG B:21 , SER B:24 , GLU B:26 , VAL D:15BINDING SITE FOR RESIDUE 18T A 303
04AC4SOFTWAREHIS A:17 , ARG A:21 , SER A:24 , GLU A:26 , HOH A:521 , GLN B:45 , ASN B:47 , ARG B:57 , HIS B:60 , LYS B:70 , ARG B:117 , LEU B:128 , TYR B:130 , TYR B:136 , GLU B:141 , ARG B:166 , HOH B:402 , HOH B:408 , HOH B:486 , HOH B:494 , HOH B:495 , VAL C:15BINDING SITE FOR RESIDUE 18T B 301
05AC5SOFTWARETHR B:62 , GLN B:68 , TYR B:136 , ALA B:137 , GLU B:141 , HOH B:487 , HOH B:491BINDING SITE FOR RESIDUE EDO B 302
06AC6SOFTWAREHIS C:17 , ASP C:19 , GLY C:22 , ARG C:23 , SER C:24 , ARG D:57 , 18T D:303BINDING SITE FOR RESIDUE EDO C 301
07AC7SOFTWAREVAL B:15 , HIS B:17 , GLN C:45 , ASN C:47 , ARG C:57 , HIS C:60 , LYS C:70 , ARG C:117 , TYR C:130 , TYR C:136 , GLU C:141 , ARG C:166 , HOH C:405 , HOH C:440 , HOH C:444 , HOH C:471 , HOH C:472 , HOH C:477 , HIS D:17 , ARG D:21 , GLU D:26 , EDO D:302BINDING SITE FOR RESIDUE 18T C 302
08AC8SOFTWAREGLN C:12 , ARG C:29 , TYR C:71 , HOH C:433BINDING SITE FOR RESIDUE EDO C 303
09AC9SOFTWAREGLN D:12 , ARG D:29 , TYR D:71 , HOH D:451BINDING SITE FOR RESIDUE EDO D 301
10BC1SOFTWAREARG C:57 , 18T C:302 , HIS D:17 , ASP D:19 , GLY D:22 , ARG D:23 , SER D:24BINDING SITE FOR RESIDUE EDO D 302
11BC2SOFTWAREVAL A:15 , HIS A:17 , HIS C:17 , ARG C:21 , GLU C:26 , EDO C:301 , HOH C:422 , GLN D:45 , ASN D:47 , ARG D:57 , HIS D:60 , LYS D:70 , ARG D:117 , TYR D:130 , TYR D:136 , GLU D:141 , ARG D:166 , HOH D:428 , HOH D:434 , HOH D:435 , HOH D:445 , HOH D:462 , HOH D:464 , HOH D:480BINDING SITE FOR RESIDUE 18T D 303

(-) SS Bonds  (0, 0)

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

(-) 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 4HMZ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HMZ)

(-) 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 d4hmza_ 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....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hmz 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:199
                                                                                                                                                                                                                                       
               SCOP domains d4hmzb_ 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....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hmz B   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGIHYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVYLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLEH 199
                                    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:200
                                                                                                                                                                                                                                        
               SCOP domains d4hmzc_ C: 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....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hmz C   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGIHYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVYLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLEHH 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200


Chain D from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains d4hmzd_ D: 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....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hmz D   1 MHPLSIEGAWSQEPVIHSDHRGRSHEWFRGESFRQAFGHDFPVAQVNVAVSHRGALRGIHYTEIPPGQAKYSVCVRGAGLDVVVDVRIGSPTFGRWEIVPMDAERNTAVYLTAGLGRAFLSLTDDATLVYLCSSGYAPAREHSVNPLDPDLGIAWPDDIEPLLSDRDENAPTLATAERLGLLPTYQAWQEQQQAQRLEHH 200
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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 4HMZ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)

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    Ile A:64 - Pro A:65   [ RasMol ]  
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  4hmz
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHMJ_STRBI | Q5SFD1: 4hn0 4hn1

(-) Related Entries Specified in the PDB File

4hn0 4hn1