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(-) Description

Title :  THE 3D STRUCTURE OF RECOMBINANT [NIFESE] HYDROGENASE FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH IN THE OXIDIZED STATE AT 1.30 ANGSTROM
 
Authors :  M. C. Marques, I. A. C. Pereira, P. M. Matias
Date :  08 May 16  (Deposition) - 22 Mar 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrogenase, Biological Hydrogen Production, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Marques, C. Tapia, O. Gutierrez-Sanz, A. R. Ramos, K. L. Keller, J. D. Wall, A. L. De Lacey, P. M. Matias, I. A. C. Pereira
The Direct Role Of Selenocysteine In [Nifese] Hydrogenase Maturation And Catalysis.
Nat. Chem. Biol. V. 13 544 2017
PubMed-ID: 28319099  |  Reference-DOI: 10.1038/NCHEMBIO.2335

(-) Compounds

Molecule 1 - PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT
    Chains: A
    EC Number: 1.12.7.2
    Engineered: YES
    Expression System: DESULFOVIBRIO VULGARIS STR. HILDENBOROUGH
    Expression System Taxid: 882
    Gene: HYSB, DVU_1917
    Organism Scientific: DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH / ATCC 29579 / NCIMB 8303)
    Organism Taxid: 882
 
Molecule 2 - PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING
    Chains: B
    EC Number: 1.12.7.2
    Engineered: YES
    Expression System: DESULFOVIBRIO VULGARIS STR. HILDENBOROUGH
    Expression System Taxid: 882
    Gene: HYSA, DVU_1918
    Organism Scientific: DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH / ATCC 29579 / NCIMB 8303)
    Organism Taxid: 882
    Other Details: CYSTEINE 75 IS OXIDIZED TO SULFENATE (CSD) IN THE CRYSTAL STRUCTURE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 11)

Asymmetric/Biological Unit (9, 11)
No.NameCountTypeFull Name
16ML1Ligand/IonOXYGEN-DAMAGED SF4
2CL1Ligand/IonCHLORIDE ION
3CSD1Mod. Amino Acid3-SULFINOALANINE
4FCO1Ligand/IonCARBONMONOXIDE-(DICYANO) IRON
5FE21Ligand/IonFE (II) ION
6H2S1Ligand/IonHYDROSULFURIC ACID
7NI1Ligand/IonNICKEL (II) ION
8SEC1Mod. Amino Acid
9SF43Ligand/IonIRON/SULFUR CLUSTER

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:208 , CYS A:211 , TYR A:213 , LEU A:214 , CYS A:232 , ARG A:233 , CYS A:238 , VAL A:260binding site for residue SF4 A 301
2AC2SOFTWARETHR A:243 , CYS A:247 , TRP A:252 , CYS A:259 , CYS A:265 , ILE A:266 , CYS A:268 , ARG B:182 , GLN B:187binding site for residue SF4 A 302
3AC3SOFTWAREGLY A:17 , CYS A:18 , CYS A:21 , GLU A:77 , GLY A:119 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , 6ML A:304 , ARG B:73 , HIS B:185binding site for residue SF4 A 303
4AC4SOFTWARECYS A:18 , THR A:19 , GLY A:20 , CYS A:21 , GLU A:77 , GLY A:78 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , SF4 A:303 , HOH A:444 , HIS B:185binding site for residue 6ML A 304
5AC5SOFTWARECYS B:78 , ALA B:420 , PRO B:421 , ARG B:422 , LEU B:425 , ALA B:444 , SER B:445 , SEC B:489 , CYS B:492 , NI B:602 , H2S B:604binding site for residue FCO B 601
6AC6SOFTWARECSD B:75 , CYS B:78 , SEC B:489 , CYS B:492 , FCO B:601 , H2S B:604binding site for residue NI B 602
7AC7SOFTWAREGLU B:56 , ILE B:441 , HIS B:495 , HOH B:723 , HOH B:730 , HOH B:753binding site for residue FE2 B 603
8AC8SOFTWARECSD B:75 , CYS B:78 , ARG B:422 , SEC B:489 , FCO B:601 , NI B:602binding site for residue H2S B 604
9AC9SOFTWARECYS B:78 , THR B:80 , ALA B:81 , PHE B:110 , ASN B:113 , PRO B:421binding site for residue CL B 605

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:78 -B:492

(-) Cis Peptide Bonds  (8, 9)

Asymmetric/Biological Unit
No.Residues
1His A:30 -Pro A:31
2Cys A:159 -Pro A:160
3Phe A:273 -Pro A:274
4Ser A:278 -Pro A:279
5Asp B:22 -Pro B:23
6Ala B:137 -Pro B:138
7Val B:140 -Pro B:141
8Met B:183 -Pro B:184

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JSH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JSH)

(-) Exons   (0, 0)

(no "Exon" information available for 5JSH)

(-) 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:283
                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee....hhhhhhhhh....hhhhhhhhh.eeee.......hhhhhhhhhhhhhhhh...eeeeee..ee.hhhhh..eeeee..eeeehhhhhhhhh..eeeeeeehhhhhhhhhhhh......eehhhhhhhhh.....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhh..hhhhh.hhhhhhhh............hhhhh.hhhhh..hhhhhh......hhhhhh..........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jsh A   1 GTLTGERPPVFWLQGQGCTGCSVTLLNSVHPSIADVLLKVISLEFHPTVMAWEGEHAIEHMRKVAEKFKGKFFLVIEGSVPVEADGKYCIIGEANHHEISMVDALKEFGPNAAAVLAVGTCAAYGGIPAAEGSETGATAVSKFLGDNGIKTPVVNIPGCPPHPDWIVGTVVLALDAIKKNGLEGGLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKYDEGVMSATFTDKVGCRYDLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQA 283
                                    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   


Chain B from PDB  Type:PROTEIN  Length:483
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeee..eeeeeeeee....hhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee..eee.......eee..eeee..eee..hhh.eeee......hhhhh..hhhhh................eeee.......hhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhh.........hhhhhhh...........hhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jsh B  13 ATGRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDPRDASQIVQRIcGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYSFVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEGTGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEALIGIPVDDIQNPVNVARLIRAFDPxLGCAVH 495
                                    22        32        42        52        62        72  |     82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482      |492   
                                                                                         75-CSD                                                                                                                                                                                                                                                                                                                                                                                                                       489-SEC
   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 5JSH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JSH)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JSH)

(-) Gene Ontology  (9, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q72AS3_DESVH | Q72AS3: 2wpn 3ze6 3ze7 3ze8 3ze9 3zea 5jsk 5jsu 5jsy 5jt1
        Q72AS4_DESVH | Q72AS4: 2wpn 3ze6 3ze7 3ze8 3ze9 3zea 5jsk 5jsu 5jsy 5jt1

(-) Related Entries Specified in the PDB File

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