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(-) Description

Title :  STRUCTURE OF THE NITROGENASE MOFE PROTEIN FROM CLOSTRIDIUM PASTEURIANUM PRESSURIZED WITH XENON
 
Authors :  C. N. Morrison, J. A. Hoy, D. C. Rees
Date :  11 Oct 14  (Deposition) - 18 Mar 15  (Release) - 01 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Xenon, Mofe Protein, Nitrogenase, Oxidoreductase (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: CLOSTRIDIUM PASTEURIANUM
    Expression System Taxid: 1501
    Gene: NIFD
    Organism Scientific: CLOSTRIDIUM PASTEURIANUM
    Organism Taxid: 1501
    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: CLOSTRIDIUM PASTEURIANUM
    Expression System Taxid: 1501
    Gene: NIFK
    Organism Scientific: CLOSTRIDIUM PASTEURIANUM
    Organism Taxid: 1501
    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  (6, 16)

Asymmetric/Biological Unit (6, 16)
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
5PRO2Mod. Amino AcidPROLINE
6XE6Ligand/IonXENON

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:182 , GLY A:464 , ILE A:465 , HIS A:482 , ICS A:602 , HOH A:724 , HOH A:729 , HOH A:733 , HOH A:737 , HOH A:741 , HOH A:745 , HOH A:777 , HOH A:800 , HOH A:825 , HOH A:954 , HOH B:688binding site for residue HCA A 601
02AC2SOFTWAREVAL A:61 , ARG A:87 , HIS A:186 , TYR A:216 , CYS A:262 , SER A:265 , GLY A:344 , GLY A:345 , ARG A:347 , PHE A:369 , HIS A:482 , HCA A:601binding site for residue ICS A 602
03AC3SOFTWAREASP A:256 , CYS A:302 , ILE A:409binding site for residue XE A 603
04AC4SOFTWARETYR A:490 , PHE A:499binding site for residue XE A 604
05AC5SOFTWARECYS A:53 , TYR A:55 , PRO A:76 , GLY A:78 , CYS A:79 , CYS A:145 , GLY A:176 , CYS B:23 , PRO B:25 , SER B:45 , GLY B:47 , CYS B:48 , TYR B:51 , HIS B:52 , THR B:105 , CYS B:106 , SER B:141binding site for residue CLF A 605
06AC6SOFTWARELEU B:15binding site for residue XE B 501
07AC7SOFTWARETYR B:30 , HIS B:59 , PHE B:178 , VAL B:179 , GLY B:180 , GLU B:323 , PHE B:411 , LYS B:424 , HOH B:662 , HOH B:675binding site for residue PRO B 502
08AC8SOFTWAREASP B:301 , ASP B:305 , HOH B:984 , LYS D:61 , GLU D:62 , HOH D:628binding site for residue FE B 503
09AC9SOFTWARELYS B:61 , GLU B:62 , HOH B:643 , ASP D:301 , ASP D:305 , HOH D:932binding site for residue FE B 504
10AD1SOFTWAREGLN C:182 , GLY C:464 , ILE C:465 , HIS C:482 , ICS C:602 , HOH C:747 , HOH C:748 , HOH C:754 , HOH C:761 , HOH C:763 , HOH C:788 , HOH C:863 , HOH C:889 , HOH C:941 , HOH D:761binding site for residue HCA C 601
11AD2SOFTWAREVAL C:61 , ARG C:87 , HIS C:186 , TYR C:216 , CYS C:262 , SER C:265 , VAL C:343 , GLY C:344 , GLY C:345 , ARG C:347 , PHE C:369 , HIS C:482 , HCA C:601binding site for residue ICS C 602
12AD3SOFTWARETYR C:490 , PHE C:499 , LEU C:503binding site for residue XE C 603
13AD4SOFTWAREASP C:256 , CYS C:302binding site for residue XE C 604
14AD5SOFTWARECYS C:53 , TYR C:55 , PRO C:76 , GLY C:78 , CYS C:79 , CYS C:145 , GLY C:176 , CYS D:23 , PRO D:25 , SER D:45 , GLY D:47 , CYS D:48 , TYR D:51 , HIS D:52 , THR D:105 , CYS D:106 , SER D:141binding site for residue CLF C 605
15AD6SOFTWARELEU D:15binding site for residue XE D 501
16AD7SOFTWARETYR D:30 , HIS D:59 , PHE D:178 , VAL D:179 , GLY D:180 , PHE D:411 , LYS D:424 , HOH D:621 , HOH D:678binding site for residue PRO D 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WN9)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Leu A:240 -Thr A:241
2Gly A:488 -Pro A:489
3Phe B:201 -Pro B:202
4Phe B:411 -Pro B:412
5Leu C:240 -Thr C:241
6Gly C:488 -Pro C:489
7Phe D:201 -Pro D:202
8Phe D:411 -Pro D:412

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WN9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WN9)

(-) Exons   (0, 0)

(no "Exon" information available for 4WN9)

(-) 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:517
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh..hhhhhhhhhh.eee.........................hhhhhhh.........eeeeee.hhhhhhh..........hhhhh........ee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh.hhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh...........eeeeeee.hhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhh.....eeee.hhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhh.........................hhhhhhhhhhhh.......hhhhhh....eee...hhhhhhhhhhhhh..eee.hhhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wn9 A   4 NLKDEILEKYIPKTKKTRSGHIVIKTEETPNPEIVANTRTVPGIITARGCAYAGCKGVVMGPIKDMVHITHGPIGCSFYTWGGRRFKSKPENGTGLNFNEYVFSTDMQESDIVFGGVNKLKDAIHEAYEMFHPAAIGVYATCPVGLIGDDILAVAATASKEIGIPVHAFSCEGYKGVSQSAGHHIANNTVMTDIIGKGNKEQKKYSINVLGEYNIGGDAWEMDRVLEKIGYHVNATLTGDATYEKVQNADKADLNLVQCHRSINYIAEMMETKYGIPWIKCNFIGVDGIVETLRDMAKCFDDPELTKRTEEVIAEEIAAIQDDLDYFKEKLQGKTACLYVGGSRSHTYMNMLKSFGVDSLVAGFEFAHRDDYEGREVIPTIKIDADSKNIPEITVTPDEQKYRVVIPEDKVEELKKAGVPLSSYGGMMKEMHDGTILIDDMNHHDMEVVLEKLKPDMFFAGIKEKFVIQKGGVLSKQLHSYDYNGPYAGFRGVVNFGHELVNGIYTPAWKMITPPWK 520
                                    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       483       493       503       513       


Chain B from PDB  Type:PROTEIN  Length:458
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee.....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh.....ee.....hhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhhhh.......eeee........hhhhhhhhhhhhhhhhhh.........eeee....hhhhhhhhhhhhhhhh..eee........................hhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhh...eeeehhhhhhhhhhhh..eee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wn9 B   1 MLDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHSHGSQGCCSYHRTVLSRHFKEPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDIIAVHTTCLSETLGDDLPTYISQMEDAGSIPEGKLVIHTNTPSYVGSHVTGFANMVQGIVNYLSENTGAKNGKINVIPGFVGPADMREIKRLFEAMDIPYIMFPDTSGVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSLGSYASDLGAKTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASIEEERGQLIDLMIDAQQYLQGKKVALLGDPDEIIALSKFIIELGAIPKYVVTGTPGMKFQKEIDAMLAEAGIEGSKVKVEGDFFDVHQWIKNEGVDLLISNTYGKFIAREENIPFVRFGFPIMDRYGHYYNPKVGYKGAIRLVEEITNVILDKIERECTEEDFEVVR 458
                                    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        


Chain C from PDB  Type:PROTEIN  Length:517
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhhhhhh.eee.........................hhhhhhh.........eeeeee.hhhhhhh..........hhhhh........ee...hhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.hhhhhhhhhhhhhh..eeee........hhhhhhhhhhhhhhhhh...........eeeeeee.hhhhhhhhhhhhhhhhh.eeeeeee...hhhhhhh.....eeee.hhhhhhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhh.........................hhhhhhhhhhh........hhhhhh....eee...hhhhhhhhhhhhh..eee.hhhhhhhhhhh........hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wn9 C   4 NLKDEILEKYIPKTKKTRSGHIVIKTEETPNPEIVANTRTVPGIITARGCAYAGCKGVVMGPIKDMVHITHGPIGCSFYTWGGRRFKSKPENGTGLNFNEYVFSTDMQESDIVFGGVNKLKDAIHEAYEMFHPAAIGVYATCPVGLIGDDILAVAATASKEIGIPVHAFSCEGYKGVSQSAGHHIANNTVMTDIIGKGNKEQKKYSINVLGEYNIGGDAWEMDRVLEKIGYHVNATLTGDATYEKVQNADKADLNLVQCHRSINYIAEMMETKYGIPWIKCNFIGVDGIVETLRDMAKCFDDPELTKRTEEVIAEEIAAIQDDLDYFKEKLQGKTACLYVGGSRSHTYMNMLKSFGVDSLVAGFEFAHRDDYEGREVIPTIKIDADSKNIPEITVTPDEQKYRVVIPEDKVEELKKAGVPLSSYGGMMKEMHDGTILIDDMNHHDMEVVLEKLKPDMFFAGIKEKFVIQKGGVLSKQLHSYDYNGPYAGFRGVVNFGHELVNGIYTPAWKMITPPWK 520
                                    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       483       493       503       513       


Chain D from PDB  Type:PROTEIN  Length:458
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee.....hhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh.....ee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhh.hhhhhhhhhhhh.......eeee........hhhhhhhhhhhhhhhhhh.........eeee....hhhhhhhhhhhhhhh...eee........................hhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhh...eeeehhhhhhhhhhhh..eee.........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wn9 D   1 MLDATPKEIVERKALRINPAKTCQPVGAMYAALGIHNCLPHSHGSQGCCSYHRTVLSRHFKEPAMASTSSFTEGASVFGGGSNIKTAVKNIFSLYNPDIIAVHTTCLSETLGDDLPTYISQMEDAGSIPEGKLVIHTNTPSYVGSHVTGFANMVQGIVNYLSENTGAKNGKINVIPGFVGPADMREIKRLFEAMDIPYIMFPDTSGVLDGPTTGEYKMYPEGGTKIEDLKDTGNSDLTLSLGSYASDLGAKTLEKKCKVPFKTLRTPIGVSATDEFIMALSEATGKEVPASIEEERGQLIDLMIDAQQYLQGKKVALLGDPDEIIALSKFIIELGAIPKYVVTGTPGMKFQKEIDAMLAEAGIEGSKVKVEGDFFDVHQWIKNEGVDLLISNTYGKFIAREENIPFVRFGFPIMDRYGHYYNPKVGYKGAIRLVEEITNVILDKIERECTEEDFEVVR 458
                                    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
   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  (0, 0)

(no "SCOP Domain" information available for 4WN9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WN9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WN9)

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  NIFK_CLOPA | P11347
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 Related Entries

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

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        NIFD_CLOPA | P00467: 1mio 4wes
        NIFK_CLOPA | P11347: 1mio 4wes

(-) Related Entries Specified in the PDB File

4wna