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(-) Description

Title :  XENON BOUND IN HYDROPHOBIC CHANNEL OF HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS
 
Authors :  S. J. Cooper, S. Bailey, P. J. Rizkallah, P. F. Lindley
Date :  27 Oct 00  (Deposition) - 25 Oct 01  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Cubane, Iron Sulfur, Thiocysteine, Prismane, Hydrophobic Cavity, S-Mercaptocysteine, Fuscoredoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Cooper, C. D. Garner, W. R. Hagen, P. F. Lindley, S. Bailey
Ferricyanide Soaked Hybrid Cluster Protein At 1. 2A And Xenon Mapping Of The Hydrophobic Cavity At 1. 8A
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYDROXYLAMINE REDUCTASE
    Chains: A
    EC Number: 1.7.-.-
    Engineered: YES
    Expression System: DESULFOVIBRIO VULGARIS
    Expression System Plasmid: PJSP104
    Expression System Strain: HILDENBOROUGH NCIMB8303
    Expression System Taxid: 881
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 881
    Strain: HILDENBOROUGH NCIMB8303
    Synonym: HYBRID CLUSTER PROTEIN, PRISMANE PROTEIN, HCP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 20)

Asymmetric/Biological Unit (8, 20)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2CSS1Mod. Amino AcidS-MERCAPTOCYSTEINE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4FSO1Ligand/IonIRON/SULFUR/OXYGEN HYBRID CLUSTER
5GOL1Ligand/IonGLYCEROL
6SF41Ligand/IonIRON/SULFUR CLUSTER
7TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
8XE13Ligand/IonXENON

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:244 , GLU A:268 , ASN A:311 , CYS A:312 , CSS A:406 , CYS A:434 , CYS A:459 , GLU A:494 , LYS A:496BINDING SITE FOR RESIDUE FSO A 600
02AC2SOFTWARECYS A:3 , PHE A:4 , GLN A:5 , CYS A:6 , THR A:9 , CYS A:15 , GLY A:19 , MET A:20 , CYS A:21 , LYS A:23 , THR A:71BINDING SITE FOR RESIDUE SF4 A 650
03AC3SOFTWARELEU A:384 , VAL A:388BINDING SITE FOR RESIDUE XE A 703
04AC4SOFTWARELEU A:501BINDING SITE FOR RESIDUE XE A 705
05AC5SOFTWAREPHE A:400BINDING SITE FOR RESIDUE XE A 706
06AC6SOFTWARELEU A:430BINDING SITE FOR RESIDUE XE A 707
07AC7SOFTWAREILE A:490 , ALA A:497BINDING SITE FOR RESIDUE XE A 709
08AC8SOFTWAREILE A:481 , TYR A:488 , LEU A:504 , VAL A:509BINDING SITE FOR RESIDUE XE A 710
09AC9SOFTWARETRP A:492 , LEU A:501BINDING SITE FOR RESIDUE XE A 711
10BC1SOFTWARESER A:462BINDING SITE FOR RESIDUE XE A 712
11BC2SOFTWAREASP A:76 , TYR A:334 , GLY A:336 , ALA A:337 , HOH A:2163 , HOH A:2619BINDING SITE FOR RESIDUE EDO A 800
12BC3SOFTWARETHR A:227 , ASN A:273 , LYS A:279 , PHE A:284 , HOH A:2498 , HOH A:2503 , HOH A:2748BINDING SITE FOR RESIDUE TRS A 803
13BC4SOFTWAREGLU A:81 , SER A:124 , THR A:125BINDING SITE FOR RESIDUE ACY A 801
14BC5SOFTWAREGLU A:181 , LYS A:201 , HOH A:2746 , HOH A:2747BINDING SITE FOR RESIDUE GOL A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1E9V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1E9V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1E9V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E9V)

(-) Exons   (0, 0)

(no "Exon" information available for 1E9V)

(-) 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 A from PDB  Type:PROTEIN  Length:553
 aligned with HCP_DESVH | P31101 from UniProtKB/Swiss-Prot  Length:553

    Alignment length:553
                                    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   
            HCP_DESVH     1 MFCFQCQETAKNTGCTVKGMCGKPEETANLQDLLIFVLRGIAIYGEKLKELGQPDRSNDDFVLQGLFATITNANWDDARFEAMISEGLARRDKLRNAFLAVYKAKNGKDFSEPLPEAATWTGDSTAFAEKAKSVGILATENEDVRSLRELLIIGLKGVAAYAEHAAVLGFRKTEIDEFMLEALASTTKDLSVDEMVALVMKAGGMAVTTMALLDEANTTTYGNPEITQVNIGVGKNPGILISGHDLKDMAELLKQTEGTGVDVYTHGEMLPANYYPAFKKYPHFVGNYGGSWWQQNPEFESFNGPILLTTNCLVPLKKENTYLDRLYTTGVVGYEGAKHIADRPAGGAKDFSALIAQAKKCPPPVEIETGSIVGGFAHHQVLALADKVVEAVKSGAIKRFVVMAGCDGRQKSRSYYTEVAENLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLDDINDLPVSYDIAWYEQKAVAVLLALLFLGVKGIRLGPTLPAFLSPNVAKVLVENFNIKPIGTVQDDIAAMMAGK 553
               SCOP domains d1e9va_ A: Hybrid cluster protein (prismane protein)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1e9vA01 A:1-139  [code=1.20.1270.20, no name defined]                                                                                      1e9vA02 A:140-223  [code=1.20.1270.20, no name defined]                             -1e9vA03 A:225-375  [code=3.40.50.2030, no name defined]                                                                                                --1e9vA04 A:378-550  [code=3.40.50.2030, no name defined]                                                                                                                      --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhh............hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhh.....hhhhhhhhhh..hhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.......eeeee...hhhhhhhhhhh.....eeee.hhhhhhhh.hhhh....eeee....hhhhhhhhhhh...eee..............hhheeee........eee...........hhhhhhhhh..........eeee...hhhhhhhhhhhhhhhhh....eeee........hhhhhhhhhhhh....eeeee..hhhhh..............eee...hhhhhhhhhhhhhhhhh.....hhh..eeeeee...hhhhhhhhhhhh......eee........hhhhhhhhhhh.......hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e9v A   1 MFCFQCQETAKNTGCTVKGMCGKPEETANLQDLLIFVLRGIAIYGEKLKELGQPDRSNDDFVLQGLFATITNANWDDARFEAMISEGLARRDKLRNAFLAVYKAKNGKDFSEPLPEAATWTGDSTAFAEKAKSVGILATENEDVRSLRELLIIGLKGVAAYAEHAAVLGFRKTEIDEFMLEALASTTKDLSVDEMVALVMKAGGMAVTTMALLDEANTTTYGNPEITQVNIGVGKNPGILISGHDLKDMAELLKQTEGTGVDVYTHGEMLPANYYPAFKKYPHFVGNYGGSWWQQNPEFESFNGPILLTTNCLVPLKKENTYLDRLYTTGVVGYEGAKHIADRPAGGAKDFSALIAQAKKCPPPVEIETGSIVGGFAHHQVLALADKVVEAVKSGAIKRFVVMAGcDGRQKSRSYYTEVAENLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLDDINDLPVSYDIAWYEQKAVAVLLALLFLGVKGIRLGPTLPAFLSPNVAKVLVENFNIKPIGTVQDDIAAMMAGK 553
                                    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   
                                                                                                                                                                                                                                                                                                                                                                                                                                               406-CSS
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E9V)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HCP_DESVH | P31101)
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:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0050418    hydroxylamine reductase activity    Catalysis of the reaction: NH3 + H2O + acceptor = hydroxylamine + reduced acceptor.
    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.
    GO:0016661    oxidoreductase activity, acting on other nitrogenous compounds as donors    Catalysis of an oxidation-reduction (redox) reaction in which a nitrogenous group, excluding NH and NH2 groups, acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1.7.-.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        HCP_DESVH | P31101: 1e1d 1e2u 1gnt 1oa1 1w9m

(-) Related Entries Specified in the PDB File

1e1d HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS
1e2u LOW TEMPERATURE STUCTURE OF HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO VULGARIS TO 1.6A