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(-) Description

Title :  CRYSTAL STRUCTURE OF AN O2-TOLERANT [NIFE]-HYDROGENASE FROM RALSTONIA EUTROPHA IN ITS AS-ISOLATED FORM WITH ASCORBATE - PARTLY REDUCED STATE
 
Authors :  M. Hammer, A. Schmidt, S. Frielingsdorf, J. Fritsch, O. Lenz, P. Scheer
Date :  20 Jan 13  (Deposition) - 02 Apr 14  (Release) - 14 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  L,S
Keywords :  [Nife] Hydrogenase, Knallgas Bacteria, Proteobacteria, Aerobic Hydrogen Bacteria, Hydrogen Catalysis, Metalloenzyme, Metalloprotein Catalytic Center, Nickel-Iron Cofactor, Bimetallic, Ni-Fe Active Site, Iron-Sulfur Cluster, [4Fe-3S] Cluster, [3Fe-4S] Cluster, [4Fe- 4S] Cluster, Reduced State, Oxidized State, Oxygen-Tolerant Hydrogenase, Membrane-Bound, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Frielingsdorf, J. Fritsch, A. Schmidt, M. Hammer, J. Lowenstein, E. Siebert, V. Pelmenschikov, T. Jaenicke, J. Kalms, Y. Rippers, F. Lendzian, I. Zebger, C. Teutloff, M. Kaupp, R. Bittl, P. Hildebrandt, B. Friedrich, O. Lenz, P. Scheerer
Reversible [4Fe-3S] Cluster Morphing In An O2-Tolerant [Nife] Hydrogenase.
Nat. Chem. Biol. V. 10 378 2014
PubMed-ID: 24705592  |  Reference-DOI: 10.1038/NCHEMBIO.1500

(-) Compounds

Molecule 1 - UPTAKE HYDROGENASE LARGE SUBUNIT
    Chains: L
    EC Number: 1.12.5.1
    Engineered: YES
    Expression System: RALSTONIA EUTROPHA
    Expression System Strain: ATCC 17699 / H16 / DSM 428 / STANIER 337
    Expression System Taxid: 381666
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-603
    Gene: HOXG, PHG002
    Organism Scientific: RALSTONIA EUTROPHA
    Organism Taxid: 381666
    Strain: ATCC 17699 / H16 / DSM 428 / STANIER 337
    Synonym: HYDROGENLYASE, MEMBRANE-BOUND HYDROGENASE LARGE SUBUNIT, HOXG
 
Molecule 2 - UPTAKE HYDROGENASE SMALL SUBUNIT
    Chains: S
    EC Number: 1.12.5.1
    Engineered: YES
    Expression System: RALSTONIA EUTROPHA
    Expression System Strain: ATCC 17699 / H16 / DSM 428 / STANIER 337
    Expression System Taxid: 381666
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 44-360
    Gene: HOXK, PHG001
    Organism Scientific: RALSTONIA EUTROPHA
    Organism Taxid: 381666
    Strain: ATCC 17699 / H16 / DSM 428 / STANIER 337
    Synonym: HYDROGENLYASE, MEMBRANE-BOUND HYDROGENASE SMALL SUBUNIT, HOXK

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : LS

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 7)

Asymmetric/Biological Unit (7, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3F3S1Ligand/IonFE3-S4 CLUSTER
4MG1Ligand/IonMAGNESIUM ION
5NFV1Ligand/IonNI-FE OXIDIZED ACTIVE CENTER
6S3F1Ligand/IonOXIDIZED [FE4-S3] CLUSTER
7SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS L:75 , CYS L:78 , CYS L:81 , HIS L:82 , ALA L:528 , PRO L:529 , ARG L:530 , LEU L:533 , VAL L:551 , PRO L:552 , THR L:553 , CSO L:597 , CYS L:600BINDING SITE FOR RESIDUE NFV L 1001
2AC2SOFTWAREGLU L:56 , CYS L:549 , HIS L:603 , HOH L:1660 , HOH L:1661 , HOH L:1662BINDING SITE FOR RESIDUE MG L 1002
3AC3SOFTWAREHIS S:187 , CYS S:190 , ARG S:193 , CYS S:215 , LEU S:216 , CYS S:221BINDING SITE FOR RESIDUE SF4 S 1001
4AC4SOFTWARELYS L:226 , THR S:226 , ASN S:228 , CYS S:230 , TRP S:235 , PRO S:242 , CYS S:249 , ILE S:250 , CYS S:252BINDING SITE FOR RESIDUE F3S S 1002
5AC5SOFTWAREHIS L:229 , CYS S:17 , THR S:18 , CYS S:19 , CYS S:20 , GLU S:76 , SER S:114 , CYS S:115 , CYS S:120 , CYS S:149BINDING SITE FOR RESIDUE S3F S 1003
6AC6SOFTWARETRP S:118 , CYS S:120 , GLY S:256BINDING SITE FOR RESIDUE CL S 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Asp L:21 -Pro L:22
2Asn L:227 -Pro L:228
3His S:29 -Pro S:30
4Lys S:125 -Pro S:126
5Cys S:149 -Pro S:150

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IUD)

(-) Sequences/Alignments

Asymmetric/Biological 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 L from PDB  Type:PROTEIN  Length:595
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4iudl_ L: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee....eeeee.........eeeeeee.....eeeeeeee....hhhhhh......hhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh..hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh.eee..eee....hhh.eee..eee..................eeee...............hhhhh............eee..eeee...........eeee.......hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iud L   3 AYATQGFNLDDRGRRIVVDPVTRIEGHMRCEVNVDANNVIRNAVSTGTMWRGLEVILKGRDPRDAWAFVERICGVCTGCHALASVRAVENALDIRIPKNAHLIREIMAKTLQVHDHAVHFYHLHALDWVDVMSALKADPKRTSELQQLVSPAHPLSSAGYFRDIQNRLKRFVESGQLGPFMNGYWGSKAYVLPPEANLMAVTHYLEALDLQKEWVKIHTIFGGKNPHPNYLVGGVPCAINLSAPVNMERLSFVKARIDEIIEFNKNVYVPDVLAIGTLYKQAGWLYGGGLAATNVLDYGEYPNVAYNKSTDQLPGGAILNGNWDEVFPVDPRDSQQVQEFVSHSWYKYADESVGLHPWDGVTEPNYVLGANTKGTRTRIEQIDESAKYSWIKSPRWRGHAMEVGPLSRYILAYAHARSGNKYAERPKEQLEYSAQMINSAIPKALGLPETQYTLKQLLPSTIGRTLARALESQYCGEMMHSDWHDLVANIRAGDTATANVDKWDPATWPLQAKGVGTVAAPRGALGHWIRIKDGRIENYQCVVPTTWNGSPRDYKGQIGAFEASLMNTPMVNPEQPVEILRTLHSFDPcLACSTH 603
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242||     258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598     
                                                                                                                                                                                                                                                                          243|                                                                                                                                                                                                                                                                                                                                                        597-CSO  
                                                                                                                                                                                                                                                                           250                                                                                                                                                                                                                                                                                                                                                                 


Chain S from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhh.....hhhhhhhhheeeeee......hhhhhhhhhhhhhhhh....eeeee.....hhhhh..ee..eehhhhhhhhhh...eeeeehhhhhh.hhhhh........hhhhhh....eeee.....hhhhhhhhhhhhhhhh..........hhhhhh.hhhhhh.hhhhhhh........hhhhhh...hhhhh.hhhhh.............................hhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4iud S   5 PRTPVLWLHGLECTCCSESFIRSAHPLAKDVVLSMISLDYDDTLMAAAGHQAEAILEEIMTKYKGNYILAVEGNPPLNQDGMSCIIGGRPFIEQLKYVAKDAKAIISWGSCASWGCVQAAKPNPTQATPVHKVITDKPIIKVPGCPPIAEVMTGVITYMLTFDRIPELDRQGRPKMFYSQRIHDKCYRRPHFDAGQFVEEWDDESARKGFCLYKMGCKGPTTYNACSTTRWNEGTSFPIQSGHGCIGCSEDGFWDKGSFYDRLTG 269
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn L:227 - Pro L:228   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        MBHL_CUPNH | P31891: 3rgw 4iub 4iuc 4ttt 5d51
        MBHS_CUPNH | P31892: 3rgw 4iub 4iuc 4ttt 5d51

(-) Related Entries Specified in the PDB File

4iub 4iuc