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(-) Description

Title :  DCMP HYDROXYMETHYLASE FROM T4 (INTACT)
 
Authors :  H. K. Song, S. H. Sohn, S. W. Suh
Date :  06 Jan 99  (Deposition) - 13 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Hydroxymethylase, Dntp Synthesizing Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. K. Song, S. H. Sohn, S. W. Suh
Crystal Structure Of Deoxycytidylate Hydroxymethylase From Bacteriophage T4, A Component Of The Deoxyribonucleoside Triphosphate-Synthesizing Complex.
Embo J. V. 18 1104 1999
PubMed-ID: 10064578  |  Reference-DOI: 10.1093/EMBOJ/18.5.1104

(-) Compounds

Molecule 1 - PROTEIN (DEOXYCYTIDYLATE HYDROXYMETHYLASE)
    Chains: A, B
    EC Number: 2.1.2.8
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: DEOXYCYTIDYLATE HYDROXYMETHYLASE, DCMP HYDROXYMETHYLASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1DCM2Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1DCM4Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1DCM2Ligand/Ion2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:28 , TYR A:96 , CYS A:148 , ARG A:168 , SER A:169 , ASN A:170 , ASP A:171 , GLY A:175 , ASP A:179 , HIS A:216 , TYR A:218 , HOH A:303 , HOH A:315 , ARG B:123 , ARG B:124BINDING SITE FOR RESIDUE DCM A 300
2AC2SOFTWAREARG A:123 , ARG A:124 , LYS B:28 , TYR B:96 , CYS B:148 , ARG B:168 , SER B:169 , ASN B:170 , ASP B:171 , GLY B:175 , ASP B:179 , HIS B:216 , TYR B:218 , HOH B:403 , HOH B:415BINDING SITE FOR RESIDUE DCM B 400
3CATAUTHORCYS A:148 , CYS B:148NULL

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B5D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1B5D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B5D)

(-) Exons   (0, 0)

(no "Exon" information available for 1B5D)

(-) 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:246
 aligned with DCHM_BPT4 | P08773 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
            DCHM_BPT4     1 MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFGALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAIWSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTNTVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDSTRQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDYVGKYA 246
               SCOP domains d1b5da_ A: dCMP hydroxymethylase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1b5dA00 A:1-246 Thymidylate Synthase, chain A                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh............eeeee.eeee...........hhhhhhhhhhhhh....hhh......hhhhh...........hhhhhh......hhhhhhhhhhh.......eee...hhhhhhhhhhh......eeeeeeeee..eeeeeeee.eee...hhhhhhhhhhhhhhhhhhhhhhh..........eeeee.eeeeehhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b5d A   1 MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFGALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAIWSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTNTVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDSTRQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDYVGKYA 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      


Chain B from PDB  Type:PROTEIN  Length:246
 aligned with DCHM_BPT4 | P08773 from UniProtKB/Swiss-Prot  Length:246

    Alignment length:246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240      
            DCHM_BPT4     1 MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFGALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAIWSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTNTVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDSTRQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDYVGKYA 246
               SCOP domains d1b5db_ B: dCMP hydroxymethylase                                                                                                                                                                                                                       SCOP domains
               CATH domains 1b5dB00 B:1-246 Thymidylate Synthase, chain A                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh............eeeee.eeee...........hhhhhhhhhhhhh....hhh......hhhhhh..........hhhhhh......hhhhhhhhhhh.......eee...hhhhhhhhhhh......eeeeeeeee..eeeeeeee.eee...hhhhhhhhhhhhhhhhhhhhhhh..........eeeee.eeeeehhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1b5d B   1 MISDSMTVEEIRLHLGLALKEKDFVVDKTGVKTIEIIGASFVADEPFIFGALNDEYIQRELEWYKSKSLFVKDIPGETPKIWQQVASSKGEINSNYGWAIWSEDNYAQYDMCLAELGQNPDSRRGIMIYTRPSMQFDYNKDGMSDFMCTNTVQYLIRDKKINAVVNMRSNDVVFGFRNDYAWQKYVLDKLVSDLNAGDSTRQYKAGSIIWNVGSLHVYSRHFYLVDHWWKTGETHISKKDYVGKYA 246
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240
   Legend:   → Mismatch (orange background)
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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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B5D)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DCHM_BPT4 | P08773)
molecular function
    GO:0047153    deoxycytidylate 5-hydroxymethyltransferase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dCMP + H(2)O = (6S)-5,6,7,8-tetrahydrofolate + 5-hydroxymethyldeoxycytidylate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

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 Related Entries

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        DCHM_BPT4 | P08773: 1b49 1b5e

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