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(-) Description

Title :  HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO DESULFURICANS X-RAY STRUCTURE AT 1.25A RESOLUTION USING SYNCHROTRON RADIATION AT A WAVELENGTH OF 0.933A
 
Authors :  S. Macedo, E. P. Mitchell, C. V. Romao, S. J. Cooper, R. Coelho, M. Y. Liu, A. V. Xavier, J. Legall, S. Bailey, D. C. Garner, W. R. Hagen, M. Teixeir M. A. Carrondo, P. Lindley
Date :  05 Oct 01  (Deposition) - 11 Apr 02  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hybrid Cluster Protein, Anaerobic Desulfovibrio Desulfuricans, Iron Anomalous (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Macedo, E. P. Mitchell, C. V. Romao, S. J. Cooper, R. Coelho, M. Y. Liu A. V. Xavier, J. Legall, S. Bailey, D. C. Garner, W. R. Hagen, M. Teixeira, M. A. Carrondo, P. Lindley
Hybrid Cluster Proteins (Hcps) From Desulfovibrio Desulfuricans Atcc 27774 And Desulfovibrio Vulgaris (Hildenborough): X-Ray Structures At 1. 25 A Resolution Using Synchrotron Radiation.
J. Biol. Inorg. Chem. V. 7 514 2002
PubMed-ID: 11941509  |  Reference-DOI: 10.1007/S00775-001-0326-Y

(-) Compounds

Molecule 1 - HYBRID CLUSTER PROTEIN
    Atcc: 27774
    Chains: A, B
    Organism Scientific: DESULFOVIBRIO DESULFURICANS
    Organism Taxid: 876
    Other Details: CUBANE CLUSTER [4FE-4S] HYBRID CLUSTER [4FE-3S-3O] PERSULPHIDE BOND BETWEEN S7 (HYBRID CLUSTER) AND S OF CYS399
    Synonym: HCP

 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, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FSO2Ligand/IonIRON/SULFUR/OXYGEN HYBRID CLUSTER
3SF42Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2FSO1Ligand/IonIRON/SULFUR/OXYGEN HYBRID CLUSTER
3SF41Ligand/IonIRON/SULFUR CLUSTER
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2FSO1Ligand/IonIRON/SULFUR/OXYGEN HYBRID CLUSTER
3SF41Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:362 , GLY A:363 , HOH A:2786 , ASP B:314 , HOH B:2528 , HOH B:2534BINDING SITE FOR RESIDUE ACT A1546
2AC2SOFTWARECYS A:6 , TYR A:7 , GLN A:8 , CYS A:9 , THR A:12 , CYS A:18 , GLY A:22 , VAL A:23 , CYS A:24 , LYS A:26 , THR A:75BINDING SITE FOR RESIDUE SF4 A1544
3AC3SOFTWAREHIS A:240 , SER A:263 , GLU A:264 , TRP A:288 , ASN A:307 , CYS A:308 , CYS A:399 , CYS A:427 , CYS A:452 , GLU A:487 , LYS A:489 , ALA A:490BINDING SITE FOR RESIDUE FSO A1545
4AC4SOFTWARECYS B:6 , TYR B:7 , GLN B:8 , CYS B:9 , THR B:12 , CYS B:18 , GLY B:22 , VAL B:23 , CYS B:24 , LYS B:26 , THR B:75BINDING SITE FOR RESIDUE SF4 B1544
5AC5SOFTWAREHIS B:240 , SER B:263 , GLU B:264 , TRP B:288 , ASN B:307 , CYS B:308 , CYS B:399 , CYS B:427 , CYS B:452 , GLU B:487 , LYS B:489 , ALA B:490BINDING SITE FOR RESIDUE FSO B1545

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:307 -Cys A:308
2Gly A:508 -Pro A:509
3Asn B:307 -Cys B:308
4Gly B:508 -Pro B:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GNL)

(-) 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:543
 aligned with HCP_DESDA | Q01770 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:543
                                    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   
            HCP_DESDA     2 SNAMFCYQCQETVGNKGCTQVGVCGKKPETAALQDALIYVTKGLGQIATRLRAEGKAVDHRIDRLVTGNLFATITNANFDDDILAERVRMTCAAKKELAASLTDKSGLSDAALWEASEKSAMLAKAGTVGVMATTDDDVRSLRWLITFGLKGMAAYAKHADVLGKHENSLDAFMQEALAKTLDDSLSVADLVALTLETGKFGVSAMALLDAANTGTYGHPEITKVNIGVGSNPGILISGHDLRDLEMLLKQTEGTGVDVYTHSEMLPAHYYPAFKKYAHFKGNYGNAWWKQKEEFESFNGPVLLTTNCLVPPKDSYKDRVYTTGIVGFTGCKHIPGEIGEHKDFSAIIAHAKTCPAPTEIESGEIIGGFAHNQVLALADKVIDAVKSGAIKKFVVMAGCDGRAKSRSYYTDFAEGLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLEDVNDLPIVYNIAWYEQKAVIVLLALLSLGVKNIHLGPTLPAFLSPNVAKVLVEQFNIGGITSPQDDLKAFF 544
               SCOP domains d1gnla_ A: Hybrid cluster protein (prismane protein)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1gnlA01 A:1-139  [code=1.20.1270.20, no name defined]                                                                                      1gnlA02 A:140-223  [code=1.20.1270.20, no name defined]                             -1gnlA03 A:225-375  [code=3.40.50.2030, no name defined]                                                                                                --1gnlA04 A:378-543  [code=3.40.50.2030, no name defined]                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhh...hhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......eeeee..hhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhh..eee........hhhhhh.eeee........eee.........hhhhhhhhhh..........eeee..hhhhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhh...eeeee.hhhhhhh......ee..ee.eee..hhhhhhhhhhhhhhhhhhh...hhhhh.eeeeee..hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gnl A   1 SNAMFCYQCQETVGNKGCTQVGVCGKKPETAALQDALIYVTKGLGQIATRLRAEGKAVDHRIDRLVTGNLFATITNANFDDDILAERVRMTCAAKKELAASLTDKSGLSDAALWEASEKSAMLAKAGTVGVMATTDDDVRSLRWLITFGLKGMAAYAKHADVLGKHENSLDAFMQEALAKTLDDSLSVADLVALTLETGKFGVSAMALLDAANTGTYGHPEITKVNIGVGSNPGILISGHDLRDLEMLLKQTEGTGVDVYTHSEMLPAHYYPAFKKYAHFKGNYGNAWWKQKEEFESFNGPVLLTTNCLVPPKDSYKDRVYTTGIVGFTGCKHIPGEIGEHKDFSAIIAHAKTCPAPTEIESGEIIGGFAHNQVLALADKVIDAVKSGAIKKFVVMAGCDGRAKSRSYYTDFAEGLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLEDVNDLPIVYNIAWYEQKAVIVLLALLSLGVKNIHLGPTLPAFLSPNVAKVLVEQFNIGGITSPQDDLKAFF 543
                                    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   


Chain B from PDB  Type:PROTEIN  Length:543
 aligned with HCP_DESDA | Q01770 from UniProtKB/Swiss-Prot  Length:545

    Alignment length:543
                                    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   
            HCP_DESDA     2 SNAMFCYQCQETVGNKGCTQVGVCGKKPETAALQDALIYVTKGLGQIATRLRAEGKAVDHRIDRLVTGNLFATITNANFDDDILAERVRMTCAAKKELAASLTDKSGLSDAALWEASEKSAMLAKAGTVGVMATTDDDVRSLRWLITFGLKGMAAYAKHADVLGKHENSLDAFMQEALAKTLDDSLSVADLVALTLETGKFGVSAMALLDAANTGTYGHPEITKVNIGVGSNPGILISGHDLRDLEMLLKQTEGTGVDVYTHSEMLPAHYYPAFKKYAHFKGNYGNAWWKQKEEFESFNGPVLLTTNCLVPPKDSYKDRVYTTGIVGFTGCKHIPGEIGEHKDFSAIIAHAKTCPAPTEIESGEIIGGFAHNQVLALADKVIDAVKSGAIKKFVVMAGCDGRAKSRSYYTDFAEGLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLEDVNDLPIVYNIAWYEQKAVIVLLALLSLGVKNIHLGPTLPAFLSPNVAKVLVEQFNIGGITSPQDDLKAFF 544
               SCOP domains d1gnlb_ B: Hybrid cluster protein (prismane protein)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1gnlB01 B:1-139  [code=1.20.1270.20, no name defined]                                                                                      1gnlB02 B:140-223  [code=1.20.1270.20, no name defined]                             -1gnlB03 B:225-375  [code=3.40.50.2030, no name defined]                                                                                                --1gnlB04 B:378-543  [code=3.40.50.2030, no name defined]                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh........hhhhhh...hhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.......eeeee..hhhhhhhhhhhhh....eeee.hhhhhhhhhhhhh....eeee...hhhhhhhhhhhhh..eee...........hhh.eeee........eee.........hhhhhhhhhh..........eeee..hhhhhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhh...eeeee.hhhhhhh......ee..ee.eee..hhhhhhhhhhhhhhhhhhh...hhhhh.eeeeee..hhhhhhhhhhhhhh.....eee.......hhhhhhhhhhhhh.....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gnl B   1 SNAMFCYQCQETVGNKGCTQVGVCGKKPETAALQDALIYVTKGLGQIATRLRAEGKAVDHRIDRLVTGNLFATITNANFDDDILAERVRMTCAAKKELAASLTDKSGLSDAALWEASEKSAMLAKAGTVGVMATTDDDVRSLRWLITFGLKGMAAYAKHADVLGKHENSLDAFMQEALAKTLDDSLSVADLVALTLETGKFGVSAMALLDAANTGTYGHPEITKVNIGVGSNPGILISGHDLRDLEMLLKQTEGTGVDVYTHSEMLPAHYYPAFKKYAHFKGNYGNAWWKQKEEFESFNGPVLLTTNCLVPPKDSYKDRVYTTGIVGFTGCKHIPGEIGEHKDFSAIIAHAKTCPAPTEIESGEIIGGFAHNQVLALADKVIDAVKSGAIKKFVVMAGCDGRAKSRSYYTDFAEGLPKDTVILTAGCAKYRYNKLNLGDIGGIPRVLDAGQCNDSYSLAVIALKLKEVFGLEDVNDLPIVYNIAWYEQKAVIVLLALLSLGVKNIHLGPTLPAFLSPNVAKVLVEQFNIGGITSPQDDLKAFF 543
                                    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
   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  (1, 2)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HCP_DESDA | Q01770)
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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 Related Entries

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

UniProtKB/Swiss-Prot
        HCP_DESDA | Q01770: 1gn9 1oa0 1upx

(-) Related Entries Specified in the PDB File

1gn9 HYBRID CLUSTER PROTEIN FROM DESULFOVIBRIO DESULFURICANS