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(-) Description

Title :  SEMISYNTHETIC [FEFE]-HYDROGENASE CPI WITH OXODITHIOLATO-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 :  1.73
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (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
    Chains: A, B
    EC Number: 1.12.7.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3) DISCR
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: CLOSTRIDIUM PASTEURIANUM
    Organism Taxid: 1501
    Synonym: CPI,FE-ONLY HYDROGENASE,[FE] HYDROGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
14WV2Ligand/IonBIS(CYANIDO-KAPPAC)(DICARBONYL)-MU-(OXOMETHYLIDENE)-MU-(OXYDIMETHANETHIOLATE-1KAPPAS:2KAPPAS)DIIRON(2+)
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL2Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION
5SF48Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (4, 14)
No.NameCountTypeFull Name
14WV2Ligand/IonBIS(CYANIDO-KAPPAC)(DICARBONYL)-MU-(OXOMETHYLIDENE)-MU-(OXYDIMETHANETHIOLATE-1KAPPAS:2KAPPAS)DIIRON(2+)
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL2Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5SF48Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
14WV1Ligand/IonBIS(CYANIDO-KAPPAC)(DICARBONYL)-MU-(OXOMETHYLIDENE)-MU-(OXYDIMETHANETHIOLATE-1KAPPAS:2KAPPAS)DIIRON(2+)
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5SF44Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:300 , PRO A:301 , CYS A:355 , CYS A:499 , CYS A:503 , GLY A:506 , 4WV 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 , ILE A:177 , CYS A:200 , PRO A:201 , VAL A:202 , 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 , LYS A:45 , 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 , MET A:497 , CYS A:503 , SF4 A:601binding site for residue 4WV A 606
07AC7SOFTWARELEU A:218 , HOH A:734 , HOH A:771 , HOH A:795 , HOH A:886 , HOH A:910binding site for residue MG A 607
08AC8SOFTWAREASN A:40 , ASP A:42 , HOH A:748 , HOH A:891 , HOH A:906 , HOH A:932binding site for residue MG A 608
09AC9SOFTWARELYS A:223 , LYS A:333 , LYS A:345 , VAL A:347 , PHE A:348 , LEU A:372 , ARG A:373 , ASP A:376 , HOH A:719binding site for residue GOL A 609
10AD1SOFTWARECYS B:300 , PRO B:301 , CYS B:355 , SER B:357 , CYS B:499 , CYS B:503 , GLY B:506 , 4WV B:606binding site for residue SF4 B 601
11AD2SOFTWARELEU B:140 , CYS 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
12AD3SOFTWARECYS 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
13AD4SOFTWAREHIS 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
14AD5SOFTWARELEU 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
15AD6SOFTWAREALA 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 4WV B 606
16AD7SOFTWARELEU B:218 , HOH B:768 , HOH B:774 , HOH B:813 , HOH B:873 , HOH B:967binding site for residue MG B 607
17AD8SOFTWAREASN B:40 , ASP B:42 , HOH B:758 , HOH B:919 , HOH B:921 , HOH B:961binding site for residue MG B 608
18AD9SOFTWARELYS B:223 , LYS B:333 , LYS B:345 , VAL B:347 , PHE B:348 , ARG B:373 , ASP B:376 , HOH B:792binding site for residue GOL B 609

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:291 -Pro A:292
2Phe A:293 -Pro A:294
3His A:579 -Pro A:580
4Gly B:291 -Pro B:292
5Phe B:293 -Pro B:294

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BYQ)

(-) 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:580
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeee.....hhhhhhhhh.......................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
                 5byq A   2 KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQ 581
                                    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       581


Chain B from PDB  Type:PROTEIN  Length:576
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeee.....hhhhhhhhh.......................eeee...eeee.hhh.....eeee..hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh..........hhhh.ee.....eeee.......hhhhhhhhhhhh....eeeee..eeeeehhhhhhhhhh.....hhhhhhh....eee..hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhh....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
                 5byq B   2 KTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAW 577
                                    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)
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    → 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 5BYQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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  PHF1_CLOPA | P29166
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  1.12.7.2
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 Related Entries

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UniProtKB/Swiss-Prot
        PHF1_CLOPA | P29166: 1c4a 1c4c 1feh 3c8y 4xdc 4xdd 5byr 5bys 5la3

(-) Related Entries Specified in the PDB File

4xdc STRUCTURE OF SAME PROTEIN WITH NATURAL, ACTIVE 2FE2S COFACTOR
4xdd STRUCTURE OF APO-PROTEIN BEFORE MATURATION