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(-) Description

Title :  STEPWISE [FEFE]-HYDROGENASE H-CLUSTER ASSEMBLY REVEALED IN THE STRUCTURE OF HYDA(DELTAEFG)
 
Authors :  D. W. Mulder, E. S. Boyd, R. Sarma, R. K. Lange, J. A. Endrizzi, J. B. Brode J. W. Peters
Date :  24 Feb 10  (Deposition) - 28 Apr 10  (Release) - 26 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrogenase, Hyda, Hydrogen, H-Cluster, [4Fe-4S] Cluster, Iron-Sulfur Cluster, Insertion, Biosynthesis, Maturation, Intermediate, Evolution, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Mulder, E. S. Boyd, R. Sarma, R. K. Lange, J. A. Endrizzi, J. B. Broderick, J. W. Peters
Stepwise [Fefe]-Hydrogenase H-Cluster Assembly Revealed In The Structure Of Hyda(Deltaefg).
Nature V. 465 248 2010
PubMed-ID: 20418861  |  Reference-DOI: 10.1038/NATURE08993

(-) Compounds

Molecule 1 - FE-HYDROGENASE
    Chains: A, B
    EC Number: 1.18.99.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET DUET
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CHLREDRAFT_183963, HYD1, HYDA, HYDA1
    Organism Scientific: CHLAMYDOMONAS REINHARDTII
    Organism Taxid: 3055
    Synonym: IRON HYDROGENASE, IRON-HYDROGENASE HYDA1

 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  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:130 , PRO A:131 , CYS A:185 , ARG A:187 , CYS A:377 , CYS A:381 , GLY A:384 , ACT A:460BINDING SITE FOR RESIDUE SF4 A 458
2AC2SOFTWAREPRO A:154 , GLN A:155 , LYS A:188BINDING SITE FOR RESIDUE CL A 459
3AC3SOFTWARECYS A:129 , CYS A:130 , MET A:375 , CYS A:381 , SF4 A:458BINDING SITE FOR RESIDUE ACT A 460
4AC4SOFTWARECYS B:130 , PRO B:131 , CYS B:185 , ARG B:187 , CYS B:377 , CYS B:381 , GLY B:384 , ACT B:460BINDING SITE FOR RESIDUE SF4 B 458
5AC5SOFTWAREPRO B:154 , GLN B:155 , LYS B:188 , HOH B:482BINDING SITE FOR RESIDUE CL B 459
6AC6SOFTWARECYS B:129 , CYS B:130 , MET B:375 , CYS B:381 , SF4 B:458BINDING SITE FOR RESIDUE ACT B 460

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LX4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Leu A:123 -Pro A:124
2Asn A:350 -Gly A:351
3Leu B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LX4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LX4)

(-) Exons   (0, 0)

(no "Exon" information available for 3LX4)

(-) 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:407
 aligned with Q9FYU1_CHLRE | Q9FYU1 from UniProtKB/TrEMBL  Length:497

    Alignment length:426
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484      
         Q9FYU1_CHLRE    65 LSHVQQALAELAKPKDDPTRKHVCVQVAPAVRVAIAETLGLAPGATTPKQLAEGLRRLGFDEVFDTLFGADLTIMEEGSELLHRLTEHLEAHPHSDEPLPMFTSCCPGWIAMLEKSYPDLIPYVSSCKSPQMMLAAMVKSYLAEKKGIAPKDMVMVSIMPCTRKQSEADRDWFCVDADPTLRQLDHVITTVELGNIFKERGINLAELPEGEWDNPMGVGSGAGVLFGTTGGVMEAALRTAYELFTGTPLPRLSLSEVRGMDGIKETNITMVPAPGSKFEELLKHRAAARAEAAAHGTPGPLAWDGGAGFTSEDGRGGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGGQPRSTDKAITQKRQAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLHTHYVAGGV 490
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhh........eeeeeehhhhhhhhhhhhh......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhh.-----....ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhh.eeeeeee...hhhhhhh.......---......eeeehhhhhhhhhhh..hhhhh.......................hhhhhhhhhhhhhhhh........ee......eeeeeeee.....hhhhhhhhhh..-----------........eee.......eeeeeeeeeehhhhhhhhhhhhhh......eeeee....hhhhh.........hhhhhhhhh..hhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lx4 A  25 LSHVQQALAELAKPKDDPTRKHVCVQVAPAVRVAIAETLGLAPGATTPKQLAEGLRRLGFDEVFDTLFGADLTIMEEGSELLHRLTEHLEA-----EPLPMFTSCCPGWIAMLEKSYPDLIPYVSSCKSPQMMLAAMVKSYLAEKKGIAPKDMVMVSIMPCTRKQSEADRDWFCVD---TLRQLDHVITTVELGNIFKERGINLAELPEGEWDNPMGVGSGAGVLFGTTGGVMEAALRTAYELFTGTPLPRLSLSEVRGMDGIKETNITMVPAPGSKFEELLKHRAA-----------GPLAWDGGAGFTSEDGRGGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGGQPRSTDKAITQKRQAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLHTHYVAGGV 450
                                    34        44        54        64        74        84        94       104       114|     |124       134       144       154       164       174       184       194     | 204       214       224       234       244       254       264       274       284       294       304      |  -       324       334       344       354       364       374       384       394       404       414       424       434       444      
                                                                                                                    115   121                                                                            200 204                                                                                                        311         323                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:407
 aligned with Q9FYU1_CHLRE | Q9FYU1 from UniProtKB/TrEMBL  Length:497

    Alignment length:426
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484      
         Q9FYU1_CHLRE    65 LSHVQQALAELAKPKDDPTRKHVCVQVAPAVRVAIAETLGLAPGATTPKQLAEGLRRLGFDEVFDTLFGADLTIMEEGSELLHRLTEHLEAHPHSDEPLPMFTSCCPGWIAMLEKSYPDLIPYVSSCKSPQMMLAAMVKSYLAEKKGIAPKDMVMVSIMPCTRKQSEADRDWFCVDADPTLRQLDHVITTVELGNIFKERGINLAELPEGEWDNPMGVGSGAGVLFGTTGGVMEAALRTAYELFTGTPLPRLSLSEVRGMDGIKETNITMVPAPGSKFEELLKHRAAARAEAAAHGTPGPLAWDGGAGFTSEDGRGGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGGQPRSTDKAITQKRQAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLHTHYVAGGV 490
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --------------------Fe_hyd_lg_C-3lx4B03 B:45-388                                                                                                                                                                                                                                                                                                                            -Fe_hyd_SSU-3lx4B01 B:390-449                                - Pfam domains (1)
           Pfam domains (2) --------------------Fe_hyd_lg_C-3lx4B04 B:45-388                                                                                                                                                                                                                                                                                                                            -Fe_hyd_SSU-3lx4B02 B:390-449                                - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhh........eeeeeehhhhhhhhhhhhh......hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhh.-----....ee...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhh.eeeeeee...hhhhhhh.......---......eeeehhhhhhhhhhh..hhhhh.......................hhhhhhhhhhhhhhhh........ee......eeeeeeee.....hhhhhhhhhh..-----------........eee.......eeeeeeeeeehhhhhhhhhhhhhh......eeeee....hhhhh.........hhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lx4 B  25 LSHVQQALAELAKPKDDPTRKHVCVQVAPAVRVAIAETLGLAPGATTPKQLAEGLRRLGFDEVFDTLFGADLTIMEEGSELLHRLTEHLEA-----EPLPMFTSCCPGWIAMLEKSYPDLIPYVSSCKSPQMMLAAMVKSYLAEKKGIAPKDMVMVSIMPCTRKQSEADRDWFCVD---TLRQLDHVITTVELGNIFKERGINLAELPEGEWDNPMGVGSGAGVLFGTTGGVMEAALRTAYELFTGTPLPRLSLSEVRGMDGIKETNITMVPAPGSKFEELLKHRAA-----------GPLAWDGGAGFTSEDGRGGITLRVAVANGLGNAKKLITKMQAGEAKYDFVEIMACPAGCVGGGGQPRSTDKAITQKRQAALYNLDEKSTLRRSHENPSIRELYDTYLGEPLGHKAHELLHTHYVAGGV 450
                                    34        44        54        64        74        84        94       104       114|     |124       134       144       154       164       174       184       194     | 204       214       224       234       244       254       264       274       284       294       304      |  -       324       334       344       354       364       374       384       394       404       414       424       434       444      
                                                                                                                    115   121                                                                            200 204                                                                                                        311         323
   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 3LX4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LX4)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Fe_hyd_SSU] (1)
(-)
Clan: no clan defined [family: Fe_hyd_lg_C] (1)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9FYU1_CHLRE | Q9FYU1)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9FYU1_CHLRE | Q9FYU1: 2n0s 4r0v

(-) Related Entries Specified in the PDB File

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