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(-) Description

Title :  CRYSTAL STRUCTURE OF A UMP/DUMP METHYLASE POLB FROM STREPTOMYCES CACAOI BOUND WITH 5-BR DUMP
 
Authors :  Y. Li, W. Chen, J. Li, Z. Xia, Z. Deng, J. Zhou
Date :  15 Mar 14  (Deposition) - 09 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Tetramer, Ump/Dump Methylase, Thyx Homolog, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Li, W. Chen, J. Li, Z. Xia, Z. Deng, J. Zhou
Crystal Structure Of A Ump/Dump Methylase Polb Form Streptomyces Cacaoi Bound With 5-Br Dump
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE THYX
    Chains: A, B, C, D
    EC Number: 2.1.1.148
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 19-257
    Gene: POLB, THYX
    Organism Scientific: STREPTOMYCES CACAOI SUBSP. ASOENSIS
    Organism Taxid: 249586
    Synonym: TSASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1BRU4Mod. Residue5-BROMO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
2FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO41Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:86 , HIS A:87 , ARG A:88 , THR A:89 , HIS A:188 , LEU A:192 , ARG A:193 , SER A:203 , HOH A:469 , HOH A:475 , ASN B:93 , GLU B:94 , SER B:96 , BRU B:301 , HOH B:464 , SER C:33 , HIS C:61 , SER C:63 , GLU C:66 , ASN C:182 , ARG C:184 , FAD C:301 , HOH C:469binding site for residue FAD A 301
2AC2SOFTWAREGLU A:94 , GLU A:95 , SER A:96 , ALA A:97 , ARG A:98 , TYR A:99 , ARG A:166 , HOH A:452 , ARG B:82 , HIS B:83 , ARG B:86 , ARG B:193 , FAD B:302 , HOH B:406 , HOH B:410binding site for residue BRU A 302
3AC3SOFTWAREARG A:100 , HOH A:449 , HOH A:482 , HOH A:496binding site for residue SO4 A 303
4AC4SOFTWAREHIS A:83 , ARG A:86 , ARG A:193 , FAD A:301 , MET B:85 , GLU B:94 , GLU B:95 , SER B:96 , ALA B:97 , ARG B:98 , TYR B:99 , ARG B:166 , HOH B:408 , HOH B:417 , HOH B:418binding site for residue BRU B 301
5AC5SOFTWAREASN A:93 , GLU A:94 , BRU A:302 , ARG B:86 , HIS B:87 , ARG B:88 , THR B:89 , HIS B:188 , LEU B:192 , ARG B:193 , SER B:203 , HIS B:204 , HOH B:448 , HOH B:452 , HOH B:463 , HOH B:482 , HOH B:491 , SER D:33 , HIS D:61 , SER D:63 , ASN D:182 , ARG D:184 , FAD D:302 , HOH D:464 , HOH D:508binding site for residue FAD B 302
6AC6SOFTWARESER A:33 , HIS A:61 , SER A:63 , ASN A:182 , ARG A:184 , FAD A:301 , ARG C:86 , HIS C:87 , ARG C:88 , THR C:89 , HIS C:188 , LEU C:192 , ARG C:193 , HOH C:437 , HOH C:461 , HOH C:477 , ASN D:93 , GLU D:94 , SER D:96 , BRU D:301 , HOH D:442binding site for residue FAD C 301
7AC7SOFTWAREGLU C:94 , GLU C:95 , SER C:96 , ALA C:97 , ARG C:98 , TYR C:99 , ARG C:166 , HOH C:424 , HOH C:470 , ARG D:82 , HIS D:83 , ARG D:86 , ARG D:193 , FAD D:302 , HOH D:421binding site for residue BRU C 302
8AC8SOFTWAREARG C:82 , HIS C:83 , ARG C:86 , ARG C:193 , FAD C:301 , GLU D:94 , GLU D:95 , SER D:96 , ALA D:97 , ARG D:98 , TYR D:99 , ARG D:166 , HOH D:416 , HOH D:417binding site for residue BRU D 301
9AC9SOFTWARESER B:33 , HIS B:61 , SER B:63 , THR B:89 , ASN B:182 , ARG B:184 , FAD B:302 , HOH B:450 , ASN C:93 , GLU C:94 , BRU C:302 , HOH C:439 , ARG D:86 , HIS D:87 , ARG D:88 , HIS D:188 , LEU D:192 , ARG D:193 , HIS D:204 , HOH D:449 , HOH D:450 , HOH D:473binding site for residue FAD D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P5B)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly C:119 -Lys C:120

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P5B)

(-) Exons   (0, 0)

(no "Exon" information available for 4P5B)

(-) 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:229
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeeeeeee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhhh....eeee..........eee......................hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5b A   6 IELRSDITVELVDSSASDLAVVKAARVSTAGEDANDGGSTRGLIRYLMRSRHGSPFEHNSMTFLVRAPIFTVRHLMRHRTWSFNEESARYREVGAAFYVPDATRLLREGKPGDYRYVGGSTDDHQQVVRSATRAYEVAFEEYQRLLDSGIAREIARLVLPVSTYSVLYATCNARALMHFLSLRTHRPDAAYVSHPQREIEMVAEQMETAWAKLMPVTHEAFTAFGRVSP 239
                                    15        25        35    ||  49        59        69        79        89        99       109      |120       130       140       150       160       170       180       190       200       210       220       230         
                                                             40|                                                                    116|                                                                                                                         
                                                              45                                                                     118                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeeeee..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhh..eeeeeeeehhhhhhhhh....eeee..........eee..hhhhhhhee....hhh.ee...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5b B   5 RIELRSDITVELVDSSASDLAVVKAARVSTAGEDANDELYDGGSTRGLIRYLMRSRHGSPFEHNSMTFLVRAPIFTVRHLMRHRTWSFNEESARYREVGAAFYVPDATRLLRQEGKPGDYRYVGGSTDDHQQVVRSATRAYEVAFEEYQRLLDSGIAREIARLVLPVSTYSVLYATCNARALMHFLSLRTHRPDAAYVSHPQREIEMVAEQMETAWAKLMPVTHEAFTAFGRVSP 239
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234     


Chain C from PDB  Type:PROTEIN  Length:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee...eeeeeeee.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee..........eee..hhhhhh.......hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p5b C   6 IELRSDITVELVDSSASDLAVVKAARVSTAGEDANDELYDGGSTRGLIRYLMRSRHGSPFEHNSMTFLVRAPIFTVRHLMRHRTWSFNEESARYREVGAAFYVPDATRLLRQEGKPGDYRYVGGSTDDHQQVVRSATRAYEVAFEEYQRLLDSGIAREIARLVLPVSTYSVLYATCNARALMHFLSLRTHRPDAAYVSHPQREIEMVAEQMETAWAKLMPVTHEAFTAFGRVSP 239
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235    


Chain D from PDB  Type:PROTEIN  Length:235
                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeeeeee.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhhh....eeee..........eee..hhhhhh.eeee..eeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5b D   5 RIELRSDITVELVDSSASDLAVVKAARVSTAGEDANDELYDGGSTRGLIRYLMRSRHGSPFEHNSMTFLVRAPIFTVRHLMRHRTWSFNEESARYREVGAAFYVPDATRLLRQEGKPGDYRYVGGSTDDHQQVVRSATRAYEVAFEEYQRLLDSGIAREIARLVLPVSTYSVLYATCNARALMHFLSLRTHRPDAAYVSHPQREIEMVAEQMETAWAKLMPVTHEAFTAFGRVSP 239
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234
   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  (0, 0)

(no "SCOP Domain" information available for 4P5B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P5B)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly C:119 - Lys C:120   [ RasMol ]  
 

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