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(-) Description

Title :  CRYSTAL STRCUTURE OF LOG FROM CORYNEBACTERIUM GLUTAMICUM
 
Authors :  H. -G. Seo, K. -J. Kim
Date :  17 Mar 16  (Deposition) - 24 Aug 16  (Release) - 24 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hydrolase, Rossmann Fold, Nucleotide-Binding Domain, Phosphoribohydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. -G. Seo, S. Kim, H. Y. Sagong, H. F. Son, K. S. Jin, I. K. Kim, K. J. Kim
Structural Basis For Cytokinin Production By Log From Corynebacterium Glutamicum
Sci Rep V. 6 31390 2016
PubMed-ID: 27507425  |  Reference-DOI: 10.1038/SREP31390

(-) Compounds

Molecule 1 - CYTOKININ RIBOSIDE 5'-MONOPHOSPHATE PHOSPHORIBOHYDROLASE
    Chains: A, B, C, D
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET30A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CGL2379
    Organism Scientific: CORYNEBACTERIUM GLUTAMICUM (STRAIN ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
    Organism Taxid: 196627
    Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:18 , SER A:19 , GLY A:116 , ALA A:117 , GLY A:118 , THR A:119 , GOL A:503 , HOH A:601 , HOH A:602 , HOH A:608 , LYS D:194binding site for residue PO4 A 501
2AC2SOFTWAREVAL A:15 , PHE A:16 , THR A:17 , TYR A:47 , GLY A:48 , MET A:55 , ARG A:99 , GLU A:122 , GOL A:503 , HOH A:608binding site for residue GOL A 502
3AC3SOFTWAREMET A:96 , ARG A:99 , PO4 A:501 , GOL A:502 , HOH A:603 , LYS D:194 , TRP D:195binding site for residue GOL A 503
4AC4SOFTWAREHIS A:84 , GLU A:85binding site for residue GOL A 504
5AC5SOFTWAREARG A:101 , ILE A:134 , SER B:76 , ASP B:95 , MET B:96binding site for residue GOL B 301
6AC6SOFTWARELYS B:194 , GLY C:18 , SER C:19 , GLY C:115 , GLY C:116 , ALA C:117 , GLY C:118 , THR C:119 , GOL C:503 , HOH C:601 , HOH C:605 , HOH C:610binding site for residue PO4 C 501
7AC7SOFTWAREVAL C:15 , PHE C:16 , THR C:17 , TYR C:47 , GLY C:48 , MET C:55 , ARG C:99 , THR C:119 , GLU C:122 , GOL C:503 , HOH C:601binding site for residue GOL C 502
8AC8SOFTWARELYS B:194 , MET C:96 , ARG C:99 , GLU C:122 , PO4 C:501 , GOL C:502 , HOH C:606binding site for residue GOL C 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ITS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ITS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ITS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ITS)

(-) Exons   (0, 0)

(no "Exon" information available for 5ITS)

(-) 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:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee........hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh...eeeeeehhhhhh........eeeee.hhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhh...hhhhhhh.eee.hhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5its A   9 TLQRVTVFTGSALGSSSLYTQAAQTLAKTAVDRGIDLVYGGGKVGLMGIVADAFLESGGEAFGVITESLMKGELGHEKLTELEIVPDMHIRKRRMAELGDGFIAMPGGAGTLEELFEVWTWQQLGIHQKPVALYDVDGFWQPLLEMLEQMTQRGFIKRDFFECLIVESDPHALLKAMQTWTPP 191
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188   


Chain B from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee........hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh...eeeeeehhhhhh........eeeee.hhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhh...hhhhhh..eee.hhhhhhhhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5its B   3 SLFDAPTLQRVTVFTGSALGSSSLYTQAAQTLAKTAVDRGIDLVYGGGKVGLMGIVADAFLESGGEAFGVITESLMKGELGHEKLTELEIVPDMHIRKRRMAELGDGFIAMPGGAGTLEELFEVWTWQQLGIHQKPVALYDVDGFWQPLLEMLEQMTQRGFIKRDFFECLIVESDPHALLKAMQTWTPPAPKWLE 197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     


Chain C from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee........hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhh...eeeeeehhhhhh........eeeee.hhhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhhhhhhhhh...hhhhhh..eee.hhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5its C   3 SLFDAPTLQRVTVFTGSALGSSSLYTQAAQTLAKTAVDRGIDLVYGGGKVGLMGIVADAFLESGGEAFGVITESLMKGELGHEKLTELEIVPDMHIRKRRMAELGDGFIAMPGGAGTLEELFEVWTWQQLGIHQKPVALYDVDGFWQPLLEMLEQMTQRGFIKRDFFECLIVESDPHALLKAMQTWTP 190
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182        


Chain D from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee.......hhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh..eeeeeehhhhh.........eeeee.hhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhh...hhhhhhhheee.hhhhhhhhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5its D   2 TSLFDAPTLQRVTVFTGSALGSSSLYTQAAQTLAKTAVDRGIDLVYGGGKVGLMGIVADAFLESGGEAFGVITESLMKGELGHEKLTELEIVPDMHIRKRRMAELGDGFIAMPGGAGTLEELFEVWTWQQLGIHQKPVALYDVDGFWQPLLEMLEQMTQRGFIKRDFFECLIVESDPHALLKAMQTWTPPAPKWLE 197
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191
   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 5ITS)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ITS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ITS)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)

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