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(-) Description

Title :  CRYSTAL STRUCTURE OF A UMP/DUMP METHYLASE POLB FROM STREPTOMYCES CACAOI BOUND WITH 5-BR UMP
 
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 :  1.76
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 From Streptomyces Cacaoi With 5-Br Ump
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  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
15BU4Ligand/Ion5-BROMO-URIDINE-5'-MONOPHOSPHATE
2FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:86 , HIS A:87 , ARG A:88 , THR A:89 , HIS A:188 , LEU A:192 , ARG A:193 , HIS A:204 , HOH A:422 , HOH A:445 , HOH A:448 , HOH A:466 , HOH A:467 , HOH A:551 , HOH A:577 , HOH A:578 , HOH A:579 , HOH A:580 , ASN B:93 , GLU B:94 , SER B:96 , 5BU B:301 , HOH B:493 , HIS C:61 , SER C:63 , GLU C:66 , THR C:89 , ASN C:182 , ARG C:184 , FAD C:301 , HOH C:454 , HOH C:546binding site for residue FAD A 301
2AC2SOFTWAREMET A:85 , GLU A:94 , GLU A:95 , SER A:96 , ALA A:97 , ARG A:98 , ARG A:166 , HOH A:427 , HOH A:442 , HOH A:453 , ARG B:82 , HIS B:83 , ARG B:86 , TYR B:124 , ARG B:193 , FAD B:302binding site for residue 5BU A 302
3AC3SOFTWAREARG A:82 , HIS A:83 , ARG A:86 , TYR A:124 , ARG A:193 , FAD A:301 , GLU B:94 , GLU B:95 , SER B:96 , ALA B:97 , ARG B:98 , ARG B:166 , HOH B:446 , HOH B:479 , HOH B:514binding site for residue 5BU B 301
4AC4SOFTWAREASN A:93 , GLU A:94 , 5BU A:302 , HOH A:462 , ARG B:86 , HIS B:87 , ARG B:88 , THR B:89 , HIS B:188 , LEU B:192 , ARG B:193 , HIS B:204 , HOH B:455 , HOH B:465 , HOH B:467 , HOH B:471 , HOH B:477 , HOH B:498 , HOH B:499 , HOH B:517 , HOH B:534 , HOH B:559 , HIS D:61 , SER D:63 , GLU D:66 , ASN D:182 , ARG D:184 , FAD D:302 , HOH D:420 , HOH D:482 , HOH D:527binding site for residue FAD B 302
5AC5SOFTWAREHIS A:61 , SER A:63 , GLU A:66 , THR A:89 , ASN A:182 , ARG A:184 , FAD A:301 , HOH A:551 , HOH A:552 , ARG C:86 , HIS C:87 , ARG C:88 , THR C:89 , HIS C:188 , LEU C:192 , ARG C:193 , HIS C:204 , HOH C:452 , HOH C:460 , HOH C:471 , HOH C:480 , HOH C:490 , HOH C:491 , HOH C:507 , HOH C:508 , HOH C:543 , HOH C:544 , HOH C:548 , HOH C:585 , ASN D:93 , GLU D:94 , 5BU D:301binding site for residue FAD C 301
6AC6SOFTWAREGLU C:94 , GLU C:95 , SER C:96 , ALA C:97 , ARG C:98 , ARG C:166 , HOH C:442 , HOH C:467 , HOH C:498 , ARG D:82 , HIS D:83 , ARG D:86 , TYR D:124 , ARG D:193 , FAD D:302binding site for residue 5BU C 302
7AC7SOFTWAREARG C:82 , HIS C:83 , ARG C:86 , TYR C:124 , ARG C:193 , FAD C:301 , MET D:85 , GLU D:94 , GLU D:95 , SER D:96 , ALA D:97 , ARG D:98 , ARG D:166 , HOH D:422 , HOH D:493binding site for residue 5BU D 301
8AC8SOFTWAREHIS B:61 , SER B:63 , GLU B:66 , THR B:89 , ASN B:182 , ARG B:184 , FAD B:302 , HOH B:517 , ASN C:93 , GLU C:94 , 5BU C:302 , HOH C:557 , ARG D:86 , HIS D:87 , ARG D:88 , THR D:89 , HIS D:188 , LEU D:192 , ARG D:193 , HOH D:442 , HOH D:444 , HOH D:445 , HOH D:458 , HOH D:462 , HOH D:466 , HOH D:519 , HOH D:527binding site for residue FAD D 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P5A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P5A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P5A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P5A)

(-) Exons   (0, 0)

(no "Exon" information available for 4P5A)

(-) 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeeee.hhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee..........eee........eee.hhhhheee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5a A   4 PRIELRSDITVELVDSSASDLAVVKAARVSTAGGSTRGLIRYLMRSRHGSPFEHNSMTFLVRAPIFTVRHLMRHRTWSFNEESARYREVGAAFYVPDATRLLRQEGKPGDYRYVGGSTDDHQQVVRSATRAYEVAFEEYQRLLDSGIAREIARLVLPVSTYSVLYATCNARALMHFLSLRTHRPDAAYVSHPQREIEMVAEQMETAWAKLMPVTHEAFTAFGRVSP 239
                                    13        23        33  ||    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233      
                                                           36|                                                                                                                                                                                                
                                                            47                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeeee.hhhhhhhhhh......hhhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee..........eee........eee.hhhhheee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5a B   4 PRIELRSDITVELVDSSASDLAVVKAARVSTYDGGSTRGLIRYLMRSRHGSPFEHNSMTFLVRAPIFTVRHLMRHRTWSFNEESARYREVGAAFYVPDATRLLRQEGKPGDYRYVGGSTDDHQQVVRSATRAYEVAFEEYQRLLDSGIAREIARLVLPVSTYSVLYATCNARALMHFLSLRTHRPDAAYVSHPQREIEMVAEQMETAWAKLMPVTHEAFTAFGRVSP 239
                                    13        23        33||      52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       
                                                         34|                                                                                                                                                                                                   
                                                          44                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eeeeeeee.hhhhhhhhhhh...hhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee..........eee........eee.hhhhheee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5a C   4 PRIELRSDITVELVDSSASDLAVVKAARVSTSTRGLIRYLMRSRHGSPFEHNSMTFLVRAPIFTVRHLMRHRTWSFNEESARYREVGAAFYVPDATRLLRQEGKPGDYRYVGGSTDDHQQVVRSATRAYEVAFEEYQRLLDSGIAREIARLVLPVSTYSVLYATCNARALMHFLSLRTHRPDAAYVSHPQREIEMVAEQMETAWAKLMPVTHEAFTAFGRVSP 239
                                    13        23        33||      56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236   
                                                         34|                                                                                                                                                                                               
                                                          48                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:225
                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eeeeeeee.hhhhhhhhhh......hhhhhhhhhhhh..hhhhhh.eeeeeeeeehhhhhhhh.....eeee..........eee........eee.hhhhheee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh....eeeeeeeehhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5a D   5 RIELRSDITVELVDSSASDLAVVKAARVSTDGGSTRGLIRYLMRSRHGSPFEHNSMTFLVRAPIFTVRHLMRHRTWSFNEESARYREVGAAFYVPDATRLLRQEGKPGDYRYVGGSTDDHQQVVRSATRAYEVAFEEYQRLLDSGIAREIARLVLPVSTYSVLYATCNARALMHFLSLRTHRPDAAYVSHPQREIEMVAEQMETAWAKLMPVTHEAFTAFGRVSP 239
                                    14        24        34|       54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234     
                                                        34|                                                                                                                                                                                                  
                                                         45
   Legend:   → Mismatch (orange background)
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    → 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 4P5A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P5A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P5A)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

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4p5b 4p5c