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(-) Description

Title :  SEMISYNTHETIC [FEFE]-HYDROGENASE CPI WITH PROPANE-DITHIOLATO-BRIDGED [2FE] COFACTOR
 
Authors :  J. Esselborn, N. Muraki, V. Engelbrecht, E. Hofmann, G. Kurisu, T. Happ
Date :  10 Jun 15  (Deposition) - 11 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrogenase, H-Cluster, Oxidoreductase, Semisynthetic Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Esselborn, N. Muraki, K. Klein, V. Engelbrecht, N. Metzler-Nolte, U. -P. Apfel, E. Hofmann, G. Kurisu, T. Happe
A Structural View Of Synthetic Cofactor Integration Into [Fefe]-Hydrogenases
Chem Sci 2015
PubMed: search  |  Reference-DOI: 10.1039/C5SC03397G

(-) Compounds

Molecule 1 - IRON HYDROGENASE 1
    ChainsA, B
    EC Number1.12.7.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System StrainBL21(DE3) DISCR
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificCLOSTRIDIUM PASTEURIANUM
    Organism Taxid1501
    SynonymCPI,FE-ONLY HYDROGENASE,[FE] HYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric Unit (5, 19)
No.NameCountTypeFull Name
14WW2Ligand/IonBIS(CYANIDO-KAPPAC)(DICARBONYL)-MU-(OXOMETHYLIDENE)[MU-PROPANE-1,3-BIS(THIOLATE)-1KAPPA~2~S~1~,S~3~:2KAPPA~2~S~1~,S~3~]DIIRON(2+)
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL2Ligand/IonGLYCEROL
4MG5Ligand/IonMAGNESIUM ION
5SF48Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
14WW1Ligand/IonBIS(CYANIDO-KAPPAC)(DICARBONYL)-MU-(OXOMETHYLIDENE)[MU-PROPANE-1,3-BIS(THIOLATE)-1KAPPA~2~S~1~,S~3~:2KAPPA~2~S~1~,S~3~]DIIRON(2+)
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL2Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5SF44Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
14WW1Ligand/IonBIS(CYANIDO-KAPPAC)(DICARBONYL)-MU-(OXOMETHYLIDENE)[MU-PROPANE-1,3-BIS(THIOLATE)-1KAPPA~2~S~1~,S~3~:2KAPPA~2~S~1~,S~3~]DIIRON(2+)
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL-1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5SF44Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:300 , PRO A:301 , CYS A:355 , CYS A:499 , CYS A:503 , GLY A:506 , 4WW A:606binding site for residue SF4 A 601
02AC2SOFTWARECYS A:157 , THR A:163 , MET A:166 , CYS A:190 , LEU A:191 , LEU A:192 , CYS A:193 , GLY A:194 , CYS A:196binding site for residue SF4 A 602
03AC3SOFTWARECYS A:147 , LEU A:148 , LEU A:149 , CYS A:150 , GLY A:151 , CYS A:153 , CYS A:200 , VAL A:202 , ALA A:204 , LEU A:205binding site for residue SF4 A 603
04AC4SOFTWAREHIS A:94 , GLU A:95 , PHE A:96 , LYS A:97 , CYS A:98 , CYS A:101 , CYS A:107 , LYS A:146 , VAL A:202 , ALA A:203binding site for residue SF4 A 604
05AC5SOFTWARELEU A:33 , CYS A:34 , PHE A:35 , CYS A:46 , GLU A:47 , CYS A:49 , CYS A:62binding site for residue FES A 605
06AC6SOFTWAREALA A:230 , PRO A:231 , SER A:232 , ILE A:268 , ALA A:272 , CYS A:299 , PRO A:324 , GLN A:325 , MET A:353 , PRO A:354 , CYS A:355 , LYS A:358 , PHE A:417 , CYS A:503 , SF4 A:601binding site for residue 4WW A 606
07AC7SOFTWARELEU A:218 , HOH A:743 , HOH A:777 , HOH A:795 , HOH A:823 , HOH A:923binding site for residue MG A 607
08AC8SOFTWAREGLU A:282 , SER A:320 , HIS A:565 , HIS A:569 , HOH A:708 , HOH A:724 , HOH A:749binding site for residue MG A 608
09AC9SOFTWAREASN A:40 , ASP A:42 , HOH A:769 , HOH A:931 , HOH A:933 , HOH A:943binding site for residue MG A 609
10AD1SOFTWARELYS A:223 , LYS A:333 , LYS A:345 , VAL A:347 , LEU A:372 , ARG A:373 , ASP A:376binding site for residue GOL A 610
11AD2SOFTWAREGLU A:444 , TYR A:445 , LYS A:446 , GLN A:447binding site for residue GOL A 611
12AD3SOFTWARECYS B:300 , PRO B:301 , CYS B:355 , CYS B:499 , CYS B:503 , GLY B:506 , 4WW B:606binding site for residue SF4 B 601
13AD4SOFTWARECYS B:157 , THR B:163 , MET B:166 , CYS B:190 , LEU B:191 , LEU B:192 , CYS B:193 , GLY B:194 , CYS B:196binding site for residue SF4 B 602
14AD5SOFTWARECYS B:147 , LEU B:148 , LEU B:149 , CYS B:150 , GLY B:151 , CYS B:153 , CYS B:200 , VAL B:202 , ALA B:204 , LEU B:205binding site for residue SF4 B 603
15AD6SOFTWAREHIS B:94 , GLU B:95 , PHE B:96 , LYS B:97 , CYS B:98 , CYS B:101 , CYS B:107 , LYS B:146 , VAL B:202 , ALA B:203binding site for residue SF4 B 604
16AD7SOFTWARELEU B:33 , CYS B:34 , PHE B:35 , LYS B:45 , CYS B:46 , GLU B:47 , CYS B:49 , CYS B:62binding site for residue FES B 605
17AD8SOFTWAREALA B:230 , PRO B:231 , SER B:232 , ILE B:268 , ALA B:272 , CYS B:299 , PRO B:324 , GLN B:325 , MET B:353 , PRO B:354 , CYS B:355 , LYS B:358 , PHE B:417 , MET B:497 , CYS B:503 , SF4 B:601binding site for residue 4WW B 606
18AD9SOFTWARELEU B:218 , HOH B:720 , HOH B:752 , HOH B:787 , HOH B:891 , HOH B:929binding site for residue MG B 607
19AE1SOFTWAREASN B:40 , ASP B:42 , HOH B:815 , HOH B:868 , HOH B:884 , HOH B:914binding site for residue MG B 608

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:291 -Pro A:292
2Phe A:293 -Pro A:294
3Gly B:291 -Pro B:292
4Phe B:293 -Pro B:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BYR)

(-) 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:571
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.....hhhhhhhh........................eeee...eeee.hhh......eee..hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..........hhhh.ee.....eeee.......hhhhhhhhhhhh....eeeee..eeeeehhhhhhhhhh.....hhhhhhh....eee..hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhh.eeeeeee..hhhhhhhh....ee..ee...eeeehhhhhhhhhhh..hhhhh.....hhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhh....eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhh....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5byr A   2 KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKY 572
                                    11        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       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571 

Chain B from PDB  Type:PROTEIN  Length:572
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...eee.....hhhhhhhhh.......................eeee...eeee.hhh......eee..hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..........hhhh.ee.....eeee.......hhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhh.....hhhhhhh....eee..hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh......hhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhh.eeeeeee..hhhhhhhh....ee..ee...eeeehhhhhhhhhhh..hhhhh.....hhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhh....eeeeeee....eeeeeeeehhhhhhhhhhhhhhhh....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5byr B   2 KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYK 573
                                    11        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       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571  

   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 5BYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHF1_CLOPA | P291661c4a 1c4c 1feh 3c8y 4xdc 4xdd 5byq 5bys 5la3

(-) Related Entries Specified in the PDB File

4xdc 4XDC CONTAINS THE SAME ENZYME WITH ITS NATURAL COFACTOR WITH AN AZA- DIMETHYL-DITHIOLATE BRIDGING THE FE ATOMS IN THE ACTIVE SITE.
4xdd 4XDD CONTAINTS THE APO-FORM OF THE SAME ENZYME.
5byq 5BYQ CONTAINS THE SAME ENZYME WITH A DIFFERENT SYNTHETIC COFACTOR IN THE ACTIVE SITE WITH AN OXO-DIMETHYL-DITHIOLATE BRIDGING THE FE ATOMS.