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(-) Description

Title :  CRYSTAL STRUCTURE OF DIPHTHINE SYNTHASE
 
Authors :  Structural Genomix
Date :  01 Dec 03  (Deposition) - 30 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Badger, J. M. Sauder, J. M. Adams, S. Antonysamy, K. Bain, M. G. Bergseid, S. G. Buchanan, M. D. Buchanan, Y. Batiyenko, J. A. Christopher, S. Emtage, A. Eroshkina, I. Feil, E. B. Furlong, K. S. Gajiwala, X. Gao, D. He, J. Hendle, A. Huber, K. Hoda, P. Kearins, C. Kissinger, B. Laubert, H. A. Lewis, J. Lin, K. Loomis, D. Lorimer, G. Louie, M. Maletic, C. D. Marsh, I. Miller, J. Molinari, H. J. Muller-Dieckmann, J. M. Newman, B. W. Noland, B. Pagarigan, F. Park, T. S. Peat, K. W. Post, S. Radojicic, A. Ramos, R. Romero, M. E. Rutter, W. E. Sanderson, K. D. Schwinn, J. Tresser, J. Winhoven, T. A. Wright, L. Wu, J. Xu, T. J. Harris
Structural Analysis Of A Set Of Proteins Resulting From A Bacterial Genomics Project
Proteins V. 60 787 2005
PubMed-ID: 16021622  |  Reference-DOI: 10.1002/PROT.20541

(-) Compounds

Molecule 1 - DIPHTHINE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DPHB, AF0381
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: DIPHTHAMIDE BIOSYNTHESIS METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1VHV)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:163 -Pro A:164
2Pro A:217 -Leu A:218
3His B:163 -Pro B:164
4Pro B:217 -Leu B:218

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1VHV)

(-) 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:251
 aligned with DPHB_ARCFU | O29866 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:251
                             1                                                                                                                                                                                                                                                         
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249 
           DPHB_ARCFU     - -MLTFVGLGLWDVKDISVKGLEAVREADEVYVEYYTSKLLSSIEEMEEFFGKRVVELERSDLEENSFRLIERAKSKSVVLLVPGDPMVATTHSAIKLEAERKGVKTRIIHGASISTAVCGLTGLHNYRFGKSATVSWHRSQTPVNVIKANRSIDAHTLLFLDLHPEPMTIGHAVENLIAEDAQMKDLYAVGIARAGSGEEVVKCDRLENLKKIDFGKPLHVMVVLAKTLHFMEFECLREFADAPAELERLV 250
               SCOP domains d1vhva_ A: Diphthine synthase, DphB                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vhvA01 A:0-111 Cobalt-precorrin-4 Transmethylase; Domain 1                                                     1vhvA02 A:112-250 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eeehhhhhh.hhhhhhhhhh..eeeeee.......hhhhhhhhhhhhh...eeee...hhhhhhhhhhh.hhhhh...eee.....hhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh.eeeeee.......eeeeee.hhhhhh......eeeee.....hhhhhhhhhhhh..hhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vhv A   0 SLLTFVGLGLWDVKDISVKGLEAVREADEVYVEYYTSKLLSSIEEmEEFFGKRVVELERSDLEENSFRLIERAKSKSVVLLVPGDPmVATTHSAIKLEAERKGVKTRIIHGASISTAVCGLTGLHNYRFGKSATVSWHRSQTPVNVIKANRSIDAHTLLFLDLHPEPmTIGHAVENLIAEDAQmKDLYAVGIARAGSGEEVVKCDRLENLKKIDFGKPLHVmVVLAKTLHFmEFECLREFADAPAELERLV 250
                                     9        19        29        39     |  49        59        69        79      | 89        99       109       119       129       139       149       159       169       179   |   189       199       209       219 |     229 |     239       249 
                                                                        45-MSE                                   86-MSE                                                                          167-MSE         183-MSE                               221-MSE   231-MSE               


Chain B from PDB  Type:PROTEIN  Length:252
 aligned with DPHB_ARCFU | O29866 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:252
                             1                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249  
           DPHB_ARCFU     - -MLTFVGLGLWDVKDISVKGLEAVREADEVYVEYYTSKLLSSIEEMEEFFGKRVVELERSDLEENSFRLIERAKSKSVVLLVPGDPMVATTHSAIKLEAERKGVKTRIIHGASISTAVCGLTGLHNYRFGKSATVSWHRSQTPVNVIKANRSIDAHTLLFLDLHPEPMTIGHAVENLIAEDAQMKDLYAVGIARAGSGEEVVKCDRLENLKKIDFGKPLHVMVVLAKTLHFMEFECLREFADAPAELERLVA 251
               SCOP domains d1vhvb_ B: Diphthine synthase, DphB                                                                                                                                                                                                                          SCOP domains
               CATH domains 1vhvB01 B:0-111 Cobalt-precorrin-4 Transmethylase; Domain 1                                                     1vhvB02 B:112-251 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                                             CATH domains
           Pfam domains (1) --TP_methylase-1vhvB01 B:2-210                                                                                                                                                                                     ----------------------------------------- Pfam domains (1)
           Pfam domains (2) --TP_methylase-1vhvB02 B:2-210                                                                                                                                                                                     ----------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhhh.eeeee........hhhhhhhhhh...eeehhhhhh.hhhhhhhhhhhheeeeee......hhhhhhhhhhhhhh...eeee...hhhhhhhhhhh.hhhhh...eee.....hhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh.eeeeee.......eeeeee.hhhhhh......eeeee.....hhhhhhhhhhhh..hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vhv B   0 SLLTFVGLGLWDVKDISVKGLEAVREADEVYVEYYTSKLLSSIEEmEEFFGKRVVELERSDLEENSFRLIERAKSKSVVLLVPGDPmVATTHSAIKLEAERKGVKTRIIHGASISTAVCGLTGLHNYRFGKSATVSWHRSQTPVNVIKANRSIDAHTLLFLDLHPEPmTIGHAVENLIAEDAQmKDLYAVGIARAGSGEEVVKCDRLENLKKIDFGKPLHVmVVLAKTLHFmEFECLREFADAPAELERLVA 251
                                     9        19        29        39     |  49        59        69        79      | 89        99       109       119       129       139       149       159       169       179   |   189       199       209       219 |     229 |     239       249  
                                                                        45-MSE                                   86-MSE                                                                          167-MSE         183-MSE                               221-MSE   231-MSE
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: TP_methylase] (35)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DPHB_ARCFU | O29866)
molecular function
    GO:0004164    diphthine synthase activity    Catalysis of the reaction: S-adenosyl-L-methionine + 2-(3-carboxy-3-aminopropyl)-L-histidine = S-adenosyl-L-homocysteine + 2-(3-carboxy-3-(methylammonio)propyl)-L-histidine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0017183    peptidyl-diphthamide biosynthetic process from peptidyl-histidine    The modification of peptidyl-histidine to 2'-(3-carboxamido-3-(trimethylammonio)propyl)-L-histidine, known as diphthamide, found in translation elongation factor EF-2. The process occurs in eukaryotes and archaea but not eubacteria.

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  Cis Peptide Bonds
    His A:163 - Pro A:164   [ RasMol ]  
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    Pro A:217 - Leu A:218   [ RasMol ]  
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