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Asym./Biol. Unit (Jmol Viewer)

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Title :   THE 3D STRUCTURE OF NI-RECONSTITUTED U489C VARIANT OF [NIFESE] HYDROGENASE FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH IN THE OXIDIZED STATE AT 1.35 ANGSTROM RESOLUTION

Authors :   M. C. Marques, I. A. C. Pereira, P. M. Matias

Date :   09 May 16 (Deposition) - 22 Mar 17 (Release) - 03 May 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym./Biol. Unit : A,B

Keywords :   Nifese-Site H2 Cleavage/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

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 STR. HILDENBOROUGH
	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
	Mutation	:	YES
	Organism Scientific	:	DESULFOVIBRIO VULGARIS STR. HILDENBOROUGH
	Organism Taxid	:	882
	Other Details	:	CYS489 IS OXIDIZED TO SULFINATE (CSD)

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (8, 10)

No.	Name	Count	Type	Full Name
1	6ML	1	Ligand/Ion	OXYGEN-DAMAGED SF4
2	CSD	1	Mod. Residue	3-SULFINOALANINE
3	CSX	1	Mod. Amino Acid	S-OXY CYSTEINE
4	FCO	1	Ligand/Ion	CARBONMONOXIDE-(DICYANO) IRON
5	FE2	1	Ligand/Ion	FE (II) ION
6	H2S	1	Ligand/Ion	HYDROSULFURIC ACID
7	NI	1	Ligand/Ion	NICKEL (II) ION
8	SF4	3	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:208 , CYS A:211 , TYR A:213 , LEU A:214 , CYS A:232 , ARG A:233 , CYS A:238 , VAL A:260	binding site for residue SF4 A 301
2	AC2	SOFTWARE	THR 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:187	binding site for residue SF4 A 302
3	AC3	SOFTWARE	GLY 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 , 6ML A:304 , ARG B:73 , HIS B:185	binding site for residue SF4 A 303
4	AC4	SOFTWARE	CYS A:18 , THR A:19 , GLY A:20 , CYS A:21 , GLU A:77 , THR A:120 , CYS A:121 , GLY A:158 , CYS A:159 , PRO A:160 , SF4 A:303 , HOH A:422 , HIS B:185	binding site for residue 6ML A 304
5	AC5	SOFTWARE	CYS B:75 , CYS B:78 , HIS B:82 , ALA B:420 , PRO B:421 , ARG B:422 , ALA B:444 , SER B:445 , CYS B:489 , CSD B:489 , CYS B:492 , NI B:602 , HOH B:1056	binding site for residue FCO B 601
6	AC6	SOFTWARE	CSX B:75 , CYS B:75 , CYS B:78 , CSD B:489 , CYS B:489 , CYS B:492 , FCO B:601 , HOH B:1056	binding site for residue NI B 602
7	AC7	SOFTWARE	GLU B:56 , ILE B:441 , HIS B:495 , HOH B:713 , HOH B:720 , HOH B:741	binding site for residue FE2 B 603
8	AC8	SOFTWARE	CYS B:78 , THR B:80 , ALA B:81 , PHE B:110 , ASN B:113 , PRO B:421	binding site for residue H2S B 604

Asymmetric/Biological Unit

No.	Residues
1	A:21	-	A:304
2	B:75	-	B:489
3	B:75	-	B:78

Asymmetric/Biological Unit

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

(no "SAP(SNP)/Variant" information available for 5JT1)

(no "PROSITE Motif" information available for 5JT1)

(no "Exon" information available for 5JT1)

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.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhh..hhhhh.hhhhhhhh............hhhhh.hhhhh..hhhhhh......hhhhhh..........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jt1 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:484
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeeeee..eeeeeeeee....hhhhhh...hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee..eee.......eee..eeee..eee..hhh.eeee......hhhhh..hhhhh................eeee.......hhhhhhhhhh...hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhh...........hhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jt1 B  13 ATGRTTIAIDPVTRIEGHLKAEVVVENGKVVDARLSGGMYRGFETILRGRDPRDASQIVQRIcCGVCPTAHSTASVLALDEAFGAKVPNNGRITRNLIFGANYLQSHILHFYHLSAQDFVQGPDTAPFVPRFPKSDLRLSKELNKAGVDQYIEALEVRRICHEMVALFGGRMPHVQGQVVGGATEIPTKEKLVEYAARFKKVRDFVEQKYVPVVYTIGSKYKDMFKVGQGFKAALCVGAFPLDNSGKKHLFMPGVYAKGKDMPFDPSKIKEYVKYSWFAEETTGLNYKEGKTIPAPDKAGAYSFVKAPRYDGLSLEVGPLARMWVNNPELSPVGKKLLKDLFGISAKKFRDLGEEAAFSLMGRHVARAEETYYMLGAIEGWLKEIKAGEDTVVMPAVPASAEGTGFTEAPRGSLLHYVKVKDSKIDNYQIVSASLWNCNPRDDMGQRGAVEEALIGIPVDDIQNPVNVARLIRAFDPCLGCAVH 495
                                    22        32        42        52        62        72  |     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    
                                                                                         75-CSX

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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 '\|'

(no "SCOP Domain" information available for 5JT1)

(no "CATH Domain" information available for 5JT1)

(no "Pfam Domain" information available for 5JT1)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala B:137 - Pro B:138	[ RasMol ]
		Asp B:22 - Pro B:23	[ RasMol ]
		Cys A:159 - Pro A:160	[ RasMol ]
		His A:30 - Pro A:31	[ RasMol ]
		Met B:183 - Pro B:184	[ RasMol ]
		Phe A:273 - Pro A:274	[ RasMol ]
		Ser A:278 - Pro A:279	[ RasMol ]
		Val B:140 - Pro B:141	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 5JT1)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 10)

Sites (8, 8)

SS Bonds (3, 3)

Cis Peptide Bonds (8, 9)

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