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(-) Description

Title :  STRUCTURE OF THE NITROGENASE MOFE PROTEIN FROM AZOTOBACTER VINELANDII PRESSURIZED WITH XENON
 
Authors :  C. N. Morrison, J. A. Hoy, L. Zhang, O. Einsle, D. C. Rees
Date :  11 Oct 14  (Deposition) - 18 Mar 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Xenon, Mofe Protein, Nitrogenase, Substrate Access, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. N. Morrison, J. A. Hoy, L. Zhang, O. Einsle, D. C. Rees
Substrate Pathways In The Nitrogenase Mofe Protein By Experimental Identification Of Small Molecule Binding Sites
Biochemistry V. 54 2052 2015
PubMed-ID: 25710326  |  Reference-DOI: 10.1021/BI501313K

(-) Compounds

Molecule 1 - NITROGENASE MOLYBDENUM-IRON PROTEIN ALPHA CHAIN
    Chains: A, C
    EC Number: 1.18.6.1
    Engineered: YES
    Expression System: AZOTOBACTER VINELANDII DJ
    Expression System Taxid: 322710
    Gene: NIFD
    Organism Scientific: AZOTOBACTER VINELANDII
    Organism Taxid: 354
    Synonym: DINITROGENASE,NITROGENASE COMPONENT I
 
Molecule 2 - NITROGENASE MOLYBDENUM-IRON PROTEIN BETA CHAIN
    Chains: B, D
    EC Number: 1.18.6.1
    Engineered: YES
    Expression System: AZOTOBACTER VINELANDII DJ
    Expression System Taxid: 322710
    Gene: NIFK
    Organism Scientific: AZOTOBACTER VINELANDII
    Organism Taxid: 354
    Synonym: DINITROGENASE,NITROGENASE COMPONENT I

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1CLF2Ligand/IonFE(8)-S(7) CLUSTER
2FE2Ligand/IonFE (III) ION
3HCA2Ligand/Ion3-HYDROXY-3-CARBOXY-ADIPIC ACID
4ICS2Ligand/IonIRON-SULFUR-MOLYBDENUM CLUSTER WITH INTERSTITIAL CARBON
5XE6Ligand/IonXENON

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:65 , GLN A:191 , GLY A:424 , ILE A:425 , HIS A:442 , ICS A:502 , HOH A:629 , HOH A:633 , HOH A:652 , HOH A:675 , HOH A:699 , HOH A:731 , HOH A:755 , HOH A:834 , HOH B:772 , HOH B:1066binding site for residue HCA A 501
02AC2SOFTWAREVAL A:70 , ARG A:96 , HIS A:195 , TYR A:229 , CYS A:275 , SER A:278 , GLY A:356 , GLY A:357 , LEU A:358 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:501binding site for residue ICS A 502
03AC3SOFTWARECYS A:62 , TYR A:64 , PRO A:85 , GLY A:87 , CYS A:88 , TYR A:91 , CYS A:154 , GLY A:185 , CYS B:70 , SER B:92 , CYS B:95 , TYR B:98 , CYS B:153 , SER B:188binding site for residue CLF A 503
04AC4SOFTWAREILE A:75 , VAL A:202binding site for residue XE A 504
05AC5SOFTWAREASP A:200binding site for residue XE A 505
06AC6SOFTWAREASP B:353 , ASP B:357 , HOH B:1022 , ARG D:108 , GLU D:109 , HOH D:720binding site for residue FE B 601
07AC7SOFTWAREARG B:108 , GLU B:109 , ASP D:353 , ASP D:357 , HOH D:715 , HOH D:877binding site for residue FE B 603
08AC8SOFTWAREALA C:65 , GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , ICS C:502 , HOH C:624 , HOH C:628 , HOH C:638 , HOH C:694 , HOH C:717 , HOH C:718 , HOH C:729 , HOH C:829 , HOH D:757 , HOH D:785binding site for residue HCA C 501
09AC9SOFTWAREVAL C:70 , ARG C:96 , HIS C:195 , TYR C:229 , CYS C:275 , GLY C:356 , GLY C:357 , LEU C:358 , ARG C:359 , PHE C:381 , HIS C:442 , HCA C:501binding site for residue ICS C 502
10AD1SOFTWARECYS C:62 , TYR C:64 , PRO C:85 , GLY C:87 , CYS C:88 , TYR C:91 , CYS C:154 , GLY C:185 , CYS D:70 , SER D:92 , CYS D:95 , TYR D:98 , CYS D:153 , SER D:188binding site for residue CLF C 503
11AD2SOFTWAREVAL C:202binding site for residue XE C 504
12AD3SOFTWAREASP C:200binding site for residue XE C 505

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Trp A:253 -Ser A:254
2Gly A:448 -Pro A:449
3Tyr B:12 -Pro B:13
4Phe B:471 -Pro B:472
5Trp C:253 -Ser C:254
6Gly C:448 -Pro C:449
7Tyr D:12 -Pro D:13
8Phe D:471 -Pro D:472

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WNA)

(-) 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:477
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhh.eee......hhhhh................hhhhhhh..........eeeee..hhhhhhh.....................ee...hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhh..hhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh...............eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh...eeeeeee...hhhhhhhhhh......eeee..hhhhhhhhhhhhh..eeeehhhhhhhhhhh...eee..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wna A   4 MSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE 480
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       


Chain B from PDB  Type:PROTEIN  Length:522
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhh.hhhhhhhhh.....ee.....hhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhh.......eeee.....hhhhhhhhhhhhhhh...eee.......................hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhh..eee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wna B   2 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 523
                                    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  


Chain C from PDB  Type:PROTEIN  Length:477
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhh.eee......hhhhh................hhhhhhh..........eeeee..hhhhhhh.....................ee...hhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhh..hhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh...............eeeeeee.hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh...eeeeeee...hhhhhhhhhh......eeee..hhhhhhhhhhhhh..eeeehhhhhhhhhhh...eee..hhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wna C   4 MSREEVESLIQEVLEVYPEKARKDRNKHLAVNDPAVTQSKKCIISNKKSQPGLMTIRGCAYAGSKGVVWGPIKDMIHISHGPVGCGQYSRAGRRNYYIGTTGVNAFVTMNFTSDFQEKDIVFGGDKKLAKLIDEVETLFPLNKGISVQSECPIGLIGDDIESVSKVKGAELSKTIVPVRCEGFRGVSQSLGHHIANDAVRDWVLGKRDEDTTFASTPYDVAIIGDYNIGGDAWSSRILLEEMGLRCVAQWSGDGSISEIELTPKVKLNLVHCYRSMNYISRHMEEKYGIPWMEYNFFGPTKTIESLRAIAAKFDESIQKKCEEVIAKYKPEWEAVVAKYRPRLEGKRVMLYIGGLRPRHVIGAYEDLGMEVVGTGYEFAHNDDYDRTMKEMGDSTLLYDDVTGYEFEEFVKRIKPDLIGSGIKEKFIFQKMGIPFREMHSWDYSGPYHGFDGFAIFARDMDMTLNNPCWKKLQAPWE 480
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       


Chain D from PDB  Type:PROTEIN  Length:522
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh.hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....ee.....hhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhh.....ee...........hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhh.hhhhh.......eeee.....hhhhhhhhhhhhhhhh..eee.......................hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhh..eee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wna D   2 SQQVDKIKASYPLFLDQDYKDMLAKKRDGFEEKYPQDKIDEVFQWTTTKEYQELNFQREALTVNPAKACQPLGAVLCALGFEKTMPYVHGSQGCVAYFRSYFNRHFREPVSCVSDSMTEDAAVFGGQQNMKDGLQNCKATYKPDMIAVSTTCMAEVIGDDLNAFINNSKKEGFIPDEFPVPFAHTPSFVGSHVTGWDNMFEGIARYFTLKSMDDKVVGSNKKINIVPGFETYLGNFRVIKRMLSEMGVGYSLLSDPEEVLDTPADGQFRMYAGGTTQEEMKDAPNALNTVLLQPWHLEKTKKFVEGTWKHEVPKLNIPMGLDWTDEFLMKVSEISGQPIPASLTKERGRLVDMMTDSHTWLHGKRFALWGDPDFVMGLVKFLLELGCEPVHILCHNGNKRWKKAVDAILAASPYGKNATVYIGKDLWHLRSLVFTDKPDFMIGNSYGKFIQRDTLHKGKEFEVPLIRIGFPIFDRHHLHRSTTLGYEGAMQILTTLVNSILERLDEETRGMQATDYNHDLVR 523
                                    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
   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 4WNA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NIFD_AZOVI | P07328: 1fp4 1g20 1g21 1l5h 1m1n 1m1y 1m34 1n2c 2afh 2afi 2min 3k1a 3min 3u7q 4nd8 4tku 4tkv 4wza 4wzb 4xpi 5bvg 5bvh 5cx1
        NIFK_AZOVI | P07329: 1fp4 1g20 1g21 1l5h 1m1n 1m1y 1m34 1n2c 2afh 2afi 2min 3k1a 3min 3u7q 4nd8 4tku 4tkv 4wza 4wzb 4xpi 5bvg 5bvh 5cx1

(-) Related Entries Specified in the PDB File

4wn9