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(-) Description

Title :  CRYSTAL STRUCTURE OF LYS187 TO ARG MUTANT OF DIPHTHINE SYNTHASE
 
Authors :  H. Mizutani, Y. Matsuura, K. Saraboji, S. M. Malathy Sony, M. N. Ponnus T. S. Kumarevel, N. Kunishima, Riken Structural Genomics/Proteom Initiative (Rsgi)
Date :  28 Jul 06  (Deposition) - 28 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Mizutani, Y. Matsuura, K. Saraboji, S. M. Malathy Sony, M. N. Ponnuswamy, T. S. Kumarevel, N. Kunishima
Crystal Structure Of Diphthine Synthase From Pyrococcus Horikoshii Ot3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPHTHINE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DPHB
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 70601
    Strain: OT3
    Synonym: DIPHTHAMIDE BIOSYNTHESIS METHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2MES3Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
4SO45Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:46 , TYR B:128 , HIS B:243BINDING SITE FOR RESIDUE SO4 B 1301
02AC2SOFTWAREARG A:60 , ALA A:91 , HOH A:1589 , LYS B:49BINDING SITE FOR RESIDUE SO4 A 1302
03AC3SOFTWARETYR A:11 , SER A:211 , LEU A:212 , ASN A:213BINDING SITE FOR RESIDUE SO4 A 1303
04AC4SOFTWAREPRO B:257 , ARG B:258 , GLU B:259BINDING SITE FOR RESIDUE SO4 B 1304
05AC5SOFTWAREARG B:46 , LYS B:129 , LYS B:241 , HIS B:243 , HOH B:1592 , HOH B:1619BINDING SITE FOR RESIDUE SO4 B 1305
06AC6SOFTWARELEU A:10 , THR A:36 , SER A:37 , GLY A:86 , ASP A:87 , VAL A:90 , SER A:115 , ILE A:116 , PHE A:165 , LEU A:166 , LEU A:206 , ARG A:208 , ALA A:209 , PRO A:233 , HIS A:234 , ILE A:235 , HOH A:1533 , HOH A:1544BINDING SITE FOR RESIDUE SAH A 1300
07AC7SOFTWAREMET A:39 , THR A:42 , THR A:43 , LEU A:44 , VAL A:57BINDING SITE FOR RESIDUE MES A 1501
08AC8SOFTWAREGLY B:86 , SER B:115 , ILE B:116 , HOH B:1506BINDING SITE FOR RESIDUE MES B 1502
09AC9SOFTWAREASP B:200 , TYR B:220 , LYS B:222 , GLU B:259BINDING SITE FOR RESIDUE MES B 1503
10BC1SOFTWARETRP A:143 , LEU B:38 , MET B:39 , THR B:42 , THR B:43 , LEU B:44BINDING SITE FOR RESIDUE GOL B 1401
11BC2SOFTWARETYR A:128 , LEU A:160 , HIS A:243 , HOH A:1639 , ASN B:66 , LYS B:132BINDING SITE FOR RESIDUE GOL A 1402
12BC3SOFTWARETHR A:43 , ARG A:46BINDING SITE FOR RESIDUE GOL A 1403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DV7)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:232 -Pro A:233
2Pro B:232 -Pro B:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DV7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DV7)

(-) Exons   (0, 0)

(no "Exon" information available for 2DV7)

(-) 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:265
 aligned with DPHB_PYRHO | O58456 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
           DPHB_PYRHO     1 MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVLSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV 265
               SCOP domains d2dv7a_ A: Diphthine synthase, DphB                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2dv7A01 A:1-114 Cobalt-precorrin-4 Transmethylase; Domain 1                                                       2dv7A02 A:115-265 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhh...eeee...hhhhhhhhhh.hhh.eeeeeee.........hhhhhhhhhhhhh..eeeeee.eehhhhee.hhhhhhhhhhhhhhhhh........eeeeee.......eeeeeehhhhh........eeeee....hhhhhhhhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dv7 A   1 MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVLSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLRVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV 265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     


Chain B from PDB  Type:PROTEIN  Length:265
 aligned with DPHB_PYRHO | O58456 from UniProtKB/Swiss-Prot  Length:265

    Alignment length:265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260     
           DPHB_PYRHO     1 MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVLSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLKVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV 265
               SCOP domains d2dv7b_ B: Diphthine synthase, DphB                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2dv7B01 B:1-114 Cobalt-precorrin-4 Transmethylase; Domain 1                                                       2dv7B02 B:115-265 Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh..eeeee.........hhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhh..eeeee...hhhhhhhhhh.hhhhh...eee.........hhhhhhhhhhhhh...eeeee.ee....ee.hhhhhhhhhhhhhhhhh........eeeeee.......eeeeeehhhhh........eeeee....hhhhhhhhhhhhh...hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dv7 B   1 MVLYFIGLGLYDERDITVKGLEIAKKCDYVFAEFYTSLMAGTTLGRIQKLIGKEIRVLSREDVELNFENIVLPLAKENDVAFLTPGDPLVATTHAELRIRAKRAGVESYVIHAPSIYSAVGITGLHIYKFGKSATVAYPEGNWFPTSYYDVIKENAERGLHTLLFLDIKAEKRMYMTANEAMELLLRVEDMKKGGVFTDDTLVVVLARAGSLNPTIRAGYVKDLIREDFGDPPHILIVPGKLHIVEAEYLVEIAGAPREILRVNV 265
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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  (0, 0)

(no "Pfam Domain" information available for 2DV7)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DPHB_PYRHO | O58456)
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:0050843    S-adenosylmethionine catabolic process    The chemical reactions and pathways resulting in the breakdown of S-adenosylmethionine, S-(5'-adenosyl)-L-methionine, an important intermediate in one-carbon metabolism.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        DPHB_PYRHO | O58456: 1vce 1wng 2dek 2dsg 2dsh 2dsi 2dv3 2dv4 2dv5 2dxv 2dxw 2dxx 2e07 2e08 2e15 2e16 2e17 2e4n 2e4r 2e7r 2e8h 2e8q 2e8r 2e8s 2ed3 2ed5 2eeq 2egb 2egl 2egs 2eh2 2eh4 2eh5 2ehc 2ehl 2ejj 2ejk 2ejz 2ek2 2ek3 2ek4 2ek7 2eka 2el0 2el1 2el2 2el3 2eld 2ele 2emr 2emu 2en5 2eni 2hr8 2huq 2hut 2huv 2hux 2owf 2owg 2owk 2owu 2owv 2p2x 2p5c 2p5f 2p6d 2p6i 2p6k 2p6l 2p9d 2pb4 2pb5 2pb6 2pca 2pcg 2pch 2pci 2pck 2pcm 2z6r

(-) Related Entries Specified in the PDB File

1wng
2dv3 THE SAME PROTEIN(L65R)
2dv4 THE SAME PROTEIN(L65Q)
2dv5 THE SAME PROTEIN(L65A) RELATED ID: PHO001000725.12 RELATED DB: TARGETDB