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(-) Description

Title :  SAM-BOUND HCGC FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  T. Fujishiro, U. Ermler, S. Shima
Date :  09 Aug 15  (Deposition) - 20 Jul 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Rossmann-Like Fold, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Fujishiro, L. Bai, T. Xu, X. Xie, M. Schick, J. Kahnt, M. Rother, X. Hu U. Ermler, S. Shima
Identification Of Hcgc As A Sam-Dependent Pyridinol Methyltransferase In [Fe]-Hydrogenase Cofactor Biosynthesis
Angew. Chem. Int. Ed. Engl. V. 55 9648 2016
PubMed-ID: 27391308  |  Reference-DOI: 10.1002/ANIE.201604352

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN MJ0489
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ROSSMANN-LIKE DOMAIN, RESIDUES 1-268
    Gene: MJ0489
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Synonym: HCGC

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1SAM4Ligand/IonS-ADENOSYLMETHIONINE
2SO416Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1SAM2Ligand/IonS-ADENOSYLMETHIONINE
2SO410Ligand/IonSULFATE ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:34 , GLY A:54 , TYR A:56 , LEU A:57 , TRP A:58 , ASP A:77 , ILE A:78 , HIS A:79 , LEU A:97 , LEU A:117 , THR A:118 , GLY A:122 , ILE A:123 , GLU A:139 , GLY A:184 , THR A:185 , SO4 A:302 , HOH A:402 , HOH A:424 , HOH A:476binding site for residue SAM A 301
02AC2SOFTWARETYR A:56 , GLY A:184 , MET A:186 , THR A:187 , SAM A:301 , HOH A:402 , HOH A:418 , HOH A:477binding site for residue SO4 A 302
03AC3SOFTWAREHIS A:79 , GLU A:80 , PHE A:81binding site for residue SO4 A 303
04AC4SOFTWAREARG A:106 , GLU A:108 , HOH A:433binding site for residue SO4 A 304
05AC5SOFTWARELYS B:34 , GLY B:54 , TYR B:56 , LEU B:57 , TRP B:58 , ASP B:77 , ILE B:78 , HIS B:79 , MET B:82 , LEU B:117 , THR B:118 , ILE B:123 , GLU B:139 , GLY B:184 , THR B:185 , SO4 B:302 , HOH B:406 , HOH B:469binding site for residue SAM B 301
06AC6SOFTWARETYR B:56 , GLY B:184 , MET B:186 , THR B:187 , SAM B:301 , HOH B:401 , HOH B:404 , HOH B:406 , HOH B:434 , HOH B:466 , HOH B:482binding site for residue SO4 B 302
07AC7SOFTWARETYR A:150 , ASP B:140 , LYS B:142 , TYR B:156 , LYS B:172 , HOH B:430 , HOH B:451binding site for residue SO4 B 303
08AC8SOFTWAREHIS B:79 , GLU B:80 , PHE B:81binding site for residue SO4 B 304
09AC9SOFTWAREASP B:225 , HIS B:227 , LYS B:228binding site for residue SO4 B 305
10AD1SOFTWAREARG B:214 , GLU B:232 , ARG D:214binding site for residue SO4 B 306
11AD2SOFTWAREARG B:178 , GLU B:199 , ASN B:256 , ASN B:257 , LEU B:260 , HOH B:403binding site for residue SO4 B 307
12AD3SOFTWARELYS C:34 , GLY C:54 , TYR C:56 , LEU C:57 , TRP C:58 , ASP C:77 , ILE C:78 , HIS C:79 , MET C:82 , LEU C:117 , THR C:118 , GLY C:122 , ILE C:123 , GLU C:139 , GLY C:184 , THR C:185 , HOH C:403binding site for residue SAM C 301
13AD4SOFTWAREASP C:140 , LYS C:142 , TYR C:156 , LYS C:172 , HOH C:422 , HOH C:469 , PHE D:145 , TYR D:150 , HOH D:451binding site for residue SO4 C 302
14AD5SOFTWAREHIS C:79 , GLU C:80 , PHE C:81binding site for residue SO4 C 303
15AD6SOFTWARETYR A:208 , TYR C:56 , GLY C:184 , MET C:186 , THR C:187 , HOH C:403 , HOH C:437binding site for residue SO4 C 304
16AD7SOFTWARELYS D:34 , GLY D:54 , TYR D:56 , LEU D:57 , TRP D:58 , ASP D:77 , ILE D:78 , HIS D:79 , MET D:82 , LEU D:117 , THR D:118 , GLY D:122 , ILE D:123 , GLU D:139 , GLY D:184 , THR D:185 , SO4 D:302 , HOH D:401 , HOH D:434binding site for residue SAM D 301
17AD8SOFTWARETYR B:208 , TYR D:56 , GLY D:184 , MET D:186 , THR D:187 , GLU D:217 , SAM D:301 , HOH D:401 , HOH D:473binding site for residue SO4 D 302
18AD9SOFTWAREHIS D:79 , GLU D:80 , PHE D:81binding site for residue SO4 D 303
19AE1SOFTWAREASN C:88 , TYR D:35 , ARG D:39 , MET D:65 , LYS D:68 , TYR D:69binding site for residue SO4 D 304
20AE2SOFTWAREASN D:110 , PRO D:111 , ASP D:112 , ASN D:132binding site for residue SO4 D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D4U)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:56 -Leu A:57
2Tyr B:56 -Leu B:57
3Tyr C:56 -Leu C:57
4Tyr D:56 -Leu D:57

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5D4U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D4U)

(-) Exons   (0, 0)

(no "Exon" information available for 5D4U)

(-) 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:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhh..eeeeeeee.hhhhhhhh.....eeeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4u A  12 EMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHEFMKGFVPNNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhh..eeeeeeee.hhhhhhhh.....eeeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhh.eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4u B  12 EMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHEFMKGFVPNNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       


Chain C from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhh..eeeeeeee.hhhhhhhh......eeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4u C  12 EMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHEFMKGFVPNNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       


Chain D from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhh..eeeeeeee.hhhhhhhh......eeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh...eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhh.eeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4u D  12 EMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHEFMKGFVPNNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261
   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 5D4U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D4U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D4U)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5D4U)

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  Y489_METJA | Q57913
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 Related Entries

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        Y489_METJA | Q57913: 5d4t 5d4v 5d5o 5d5t

(-) Related Entries Specified in the PDB File

5d4t