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(-) Description

Title :  HCGC WITH SAH AND A GUANYLYLPYRIDINOL (GP) DERIVATIVE
 
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 :  1.60
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  (3, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SO418Ligand/IonSULFATE ION
3YGP2Ligand/Ion5'-O-[(R)-[(3,6-DIMETHYL-2-OXO-1,2-DIHYDROPYRIDIN-4-YL)OXY](HYDROXY)PHOSPHORYL]GUANOSINE
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SO49Ligand/IonSULFATE ION
3YGP1Ligand/Ion5'-O-[(R)-[(3,6-DIMETHYL-2-OXO-1,2-DIHYDROPYRIDIN-4-YL)OXY](HYDROXY)PHOSPHORYL]GUANOSINE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2SO49Ligand/IonSULFATE ION
3YGP1Ligand/Ion5'-O-[(R)-[(3,6-DIMETHYL-2-OXO-1,2-DIHYDROPYRIDIN-4-YL)OXY](HYDROXY)PHOSPHORYL]GUANOSINE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:34 , GLY A:54 , VAL A:55 , TYR A:56 , LEU A:57 , TRP A:58 , ASP A:77 , ILE A:78 , HIS A:79 , MET A:82 , LEU A:117 , THR A:118 , ILE A:123 , GLU A:139 , GLY A:184 , THR A:185 , HOH A:433 , HOH A:533 , HOH A:544 , HOH A:557 , HOH C:430binding site for residue SAH A 301
02AC2SOFTWAREHIS A:79 , GLU A:80 , PHE A:81 , HOH A:431 , HOH A:554binding site for residue SO4 A 302
03AC3SOFTWAREARG A:214 , SER A:231 , GLU A:232 , HOH A:412 , HOH A:422 , HOH A:435 , HOH A:444binding site for residue SO4 A 303
04AC4SOFTWARETYR A:35 , ARG A:39 , LYS A:68 , TYR A:69binding site for residue SO4 A 304
05AC5SOFTWARELYS B:34 , GLY B:54 , VAL B:55 , 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 , HOH B:474 , HOH B:506 , HOH B:545binding site for residue SAH B 301
06AC6SOFTWARETYR A:150 , HOH A:423 , HOH A:445 , ASP B:140 , LYS B:142 , TYR B:156 , LYS B:172 , YGP B:307 , HOH B:446 , HOH B:516binding site for residue SO4 B 302
07AC7SOFTWAREHIS B:79 , GLU B:80 , PHE B:81binding site for residue SO4 B 303
08AC8SOFTWARETYR B:56 , GLY B:184 , MET B:186 , THR B:187 , GLU B:217 , HOH B:474 , HOH B:545binding site for residue SO4 B 304
09AC9SOFTWAREARG B:22 , HOH B:534 , HOH B:556binding site for residue SO4 B 305
10AD1SOFTWAREASP B:225 , HIS B:227 , LYS B:228binding site for residue SO4 B 306
11AD2SOFTWARETYR A:156 , LYS A:172 , GLU A:266 , HOH A:423 , TYR B:156 , LYS B:157 , ALA B:160 , GLU B:266 , SO4 B:302 , HOH B:424 , HOH B:516binding site for residue YGP B 307
12AD3SOFTWARELYS C:34 , GLY C:54 , VAL C:55 , 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 , ILE C:123 , GLU C:139 , GLY C:184 , THR C:185 , HOH C:447 , HOH C:452 , HOH C:480 , HOH C:514 , HOH C:560binding site for residue SAH C 301
13AD4SOFTWAREILE C:78 , HIS C:79 , GLU C:80 , PHE C:81binding site for residue SO4 C 302
14AD5SOFTWAREHOH A:513 , TYR C:56 , GLY C:184 , MET C:186 , THR C:187 , HOH C:415 , HOH C:452 , HOH C:560binding site for residue SO4 C 303
15AD6SOFTWAREARG C:214 , SER C:231 , GLU C:232 , HOH C:413 , HOH C:420 , HOH C:507binding site for residue SO4 C 304
16AD7SOFTWAREASP C:140 , LYS C:142 , TYR C:156 , LYS C:172 , YGP C:308 , HOH C:422 , HOH C:432 , HOH C:556 , HOH D:552binding site for residue SO4 C 305
17AD8SOFTWAREARG C:22 , HOH C:484binding site for residue SO4 C 306
18AD9SOFTWAREHIS C:227binding site for residue SO4 C 307
19AE1SOFTWARETYR C:156 , LYS C:157 , ALA C:160 , GLU C:266 , SO4 C:305 , HOH C:406 , HOH C:428 , HOH C:565 , TYR D:156 , LYS D:172 , GLU D:266 , HOH D:552binding site for residue YGP C 308
20AE2SOFTWARELYS D:34 , GLY D:54 , VAL D:55 , TYR D:56 , LEU D:57 , TRP D:58 , ASP D:77 , ILE D:78 , HIS D:79 , MET D:82 , LEU D:97 , LEU D:117 , THR D:118 , ILE D:123 , GLU D:139 , GLY D:184 , THR D:185 , HOH D:453 , HOH D:476 , HOH D:530binding site for residue SAH D 301
21AE3SOFTWARELYS D:72 , TYR D:74 , LYS D:93 , LYS D:103 , HOH D:424 , HOH D:443 , HOH D:546binding site for residue SO4 D 302
22AE4SOFTWARETYR D:35 , ARG D:39 , MET D:65 , LYS D:68 , TYR D:69 , HOH D:481binding site for residue SO4 D 303
23AE5SOFTWAREHOH B:477 , TYR D:56 , GLY D:184 , MET D:186 , THR D:187 , HOH D:404 , HOH D:425 , HOH D:476binding site for residue SO4 D 304
24AE6SOFTWAREHIS D:79 , GLU D:80 , PHE D:81 , HOH D:457 , HOH D:501binding site for residue SO4 D 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5D4V)

(-) 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 5D4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5D4V)

(-) Exons   (0, 0)

(no "Exon" information available for 5D4V)

(-) 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......eeeehhhhhhhhhh......eeee.......hhhhhh.....eeeee......hhhhhhhhhhhhhhh......eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4v 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:260
                                                                                                                                                                                                                                                                                                    
               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......hhhhhhhhhhhhhhh......eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhh.eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4v B   9 GITEMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHEFMKGFVPNNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268


Chain C from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               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
                 5d4v C   9 GITEMVKTIDTKTRVVDVTNEIAKKKYQAIRDFLEGEEFKEVVIFGVYLWGNYTAQMLSKYADKVYLVDIHEFMKGFVPNNNSIKFLNLNEFKLKFIRGEVNPDLIVDLTGLGGIEPEFLAKFNPKVFIVEDPKGVFDVDIYEADNTYKRTAPFIEKAKVGVLKTYRKARVSKTSGTMTLTIDTIVDASREITSLDGVLYAIPNLRYYEGILFHENDIHKFLSEISQPAITISTLNDVLDEAEEILSNNINLIYSFVEEL 268
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268


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......hhhhhhhhhhhhhhh......eeeeeeeee........hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh..hhhhhhhhhh...eeeee...hhhhhhhhhhhhhhheeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5d4v 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)
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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  (0, 0)

(no "SCOP Domain" information available for 5D4V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5D4V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5D4V)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5D4V)

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  Y489_METJA | Q57913
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 Related Entries

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        Y489_METJA | Q57913: 5d4t 5d4u 5d5o 5d5t

(-) Related Entries Specified in the PDB File

5d4t 5d4u