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(-) Description

Title :  APO [FEFE]-HYDROGENASE CPI
 
Authors :  J. Esselborn, E. Hofmann, G. Kurisu, T. Happe
Date :  19 Dec 14  (Deposition) - 11 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cpi, Fefe-Hydrogenase, Oxidoreductase (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 Taxid: 562
    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): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 21)

Asymmetric Unit (5, 21)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL3Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION
5SF48Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL1Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5SF44Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FES1Ligand/IonFE2/S2 (INORGANIC) CLUSTER
3GOL2Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5SF44Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:300 , PRO A:301 , CYS A:355 , ALA A:498 , CYS A:499 , CYS A:503 , GLY A:506binding 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 , 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:218 , HOH A:887 , HOH A:905 , HOH A:749 , HOH A:1071 , HOH A:758binding site for residue MG A 605
06AC6SOFTWARELEU 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 606
07AC7SOFTWAREASN A:40 , ASP A:42 , HOH A:871 , HOH A:1085 , HOH A:1095 , HOH A:1111binding site for residue MG A 607
08AC8SOFTWAREALA A:230 , PRO A:231 , SER A:232 , CYS A:503binding site for residue CL A 608
09AC9SOFTWARELYS A:223 , LYS A:333 , LYS A:345 , VAL A:347 , LEU A:372 , ARG A:373 , ASP A:376 , HOH A:704 , HOH A:873binding site for residue GOL A 609
10AD1SOFTWAREASP A:404 , PRO A:405 , ALA A:406 , HOH A:1281 , HOH A:1333binding site for residue CL A 610
11AD2SOFTWARECYS B:300 , PRO B:301 , CYS B:355 , ALA B:498 , CYS B:499 , CYS B:503 , GLY B:506binding site for residue SF4 B 601
12AD3SOFTWARECYS 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
13AD4SOFTWARECYS B:147 , LEU B:148 , LEU B:149 , CYS B:150 , GLY B:151 , CYS B:153 , CYS B:200 , VAL B:202 , LEU B:205binding site for residue SF4 B 603
14AD5SOFTWAREHIS B:94 , GLU B:95 , 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
15AD6SOFTWARELEU B:33 , CYS B:34 , PHE B:35 , ASN B:40 , LYS B:45 , CYS B:46 , GLU B:47 , CYS B:49 , CYS B:62binding site for residue FES B 605
16AD7SOFTWAREALA B:230 , PRO B:231 , SER B:232 , CYS B:503binding site for residue CL B 606
17AD8SOFTWAREASP B:404 , PRO B:405 , ALA B:406 , HOH B:1278 , HOH B:1312binding site for residue CL B 607
18AD9SOFTWARELEU B:218 , HOH B:711 , HOH B:879 , HOH B:954 , HOH B:994 , HOH B:735binding site for residue MG B 608
19AE1SOFTWAREASN B:40 , ASP B:42 , HOH B:899 , HOH B:1052 , HOH B:1081 , HOH B:1097binding site for residue MG B 609
20AE2SOFTWARELYS B:223 , LYS B:333 , LYS B:345 , VAL B:347 , PHE B:348 , LEU B:372 , ARG B:373 , ASP B:376 , HOH B:855 , HOH B:869binding site for residue GOL B 610
21AE3SOFTWAREGLN B:366 , PHE B:570 , LYS B:571binding site for residue GOL B 611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XDD)

(-) Cis Peptide Bonds  (5, 5)

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
5His B:579 -Pro B:580

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XDD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XDD)

(-) Exons   (0, 0)

(no "Exon" information available for 4XDD)

(-) 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:582
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeeee....hhhhhhhhh.......................eeee...eeee.hhh......eee..hhhhhhhhhhhhhhhhh..............hhhhhhhhhhh...........hhh.ee.....eeee.hhh...hhhhhhhhhhhh....eeeee..eeeeehhhhhhhhhh.....hhhhhhh....eee..hhhhhhhhhhh...eeeeee.hhhhhhhhhhhh......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhh.eeeeeee..hhhhhhhh....ee..ee...eeeehhhhhhhhhhh..hhhhh.....hhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhh.......hhhhh....eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhhh....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xdd A   1 MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQF 582
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580  


Chain B from PDB  Type:PROTEIN  Length:581
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee....hhhhhhhhh.......................eeee...eeee.hhh......eee..hhhhhhhhhhhhhhhhh..............hhhhhhhhhh............hhh.ee.....eeee.hhh...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.....hhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xdd B   1 MKTIIINGVQFNTDEDTTILKFARDNNIDISALCFLNNCNNDINKCEICTVEVEGTGLVTACDTLIEDGMIINTNSDAVNEKIKSRISQLLDIHEFKCGPCNRRENCEFLKLVIKYKARASKPFLPKDKTEYVDERSKSLTVDRTKCLLCGRCVNACGKNTETYAMKFLNKNGKTIIGAEDEKCFDDTNCLLCGQCIIACPVAALSEKSHMDRVKNALNAPEKHVIVAMAPSVRASIGELFNMGFGVDVTGKIYTALRQLGFDKIFDINFGADMTIMEEATELVQRIENNGPFPMFTSCCPGWVRQAENYYPELLNNLSSAKSPQQIFGTASKTYYPSISGLDPKNVFTVTVMPCTSKKFEADRPQMEKDGLRDIDAVITTRELAKMIKDAKIPFAKLEDSEADPAMGEYSGAGAIFGATGGVMEAALRSAKDFAENAELEDIEYKQVRGLNGIKEAEVEINNNKYNVAVINGASNLFKFMKSGMINEKQYHFIEVMACHGGCVNGGGQPHVNPKDLEKVDIKKVRASVLYNQDEHLSKRKSHENTALVKMYQNYFGKPGEGRAHEILHFKYKKSAWSHPQ 581
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580
   Legend:   → Mismatch (orange background)
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  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 4XDD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XDD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XDD)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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        PHF1_CLOPA | P29166: 1c4a 1c4c 1feh 3c8y 4xdc 5byq 5byr 5bys 5la3

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