2RAB - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF GLUTATHIONE AMIDE REDUCTASE FROM CHROMATIUM GRACILE IN COMPLEX WITH NAD

Authors :   F. Van Petegem, D. De Vos, S. Savvides, B. Vergauwen, J. Van Beeumen

Date :   14 Sep 07 (Deposition) - 19 Feb 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Glutathione, Substrate Analog, Nad, Fad, Redox, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Van Petegem, D. De Vos, S. Savvides, B. Vergauwen, J. Van Beeumen
Understanding Nicotinamide Dinucleotide Cofactor And Substrate Specificity In Class I Flavoprotein Disulfide Oxidoreductases: Crystallographic Analysis Of A Glutathione Amide Reductase.
J. Mol. Biol. V. 374 883 2007
PubMed-ID: 17977556 | Reference-DOI: 10.1016/J.JMB.2007.09.072

Molecule 1 - GLUTATHIONE AMIDE REDUCTASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organism Scientific	:	MARICHROMATIUM GRACILE
	Organism Taxid	:	1048

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 16)

No.	Name	Count	Type	Full Name
1	CL	8	Ligand/Ion	CHLORIDE ION
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
4	NI	4	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:11 , GLY A:13 , SER A:14 , GLY A:15 , ILE A:33 , GLU A:34 , SER A:35 , GLY A:40 , THR A:41 , VAL A:45 , GLY A:46 , CYS A:47 , LYS A:50 , GLY A:112 , HIS A:113 , ALA A:114 , ALA A:137 , THR A:138 , GLY A:139 , ARG A:262 , LEU A:269 , GLY A:301 , ASP A:302 , GLN A:308 , LEU A:309 , THR A:310 , PRO A:311 , NAD A:600 , HOH A:601 , HOH A:605 , HOH A:608 , HOH A:645 , HOH A:776 , HOH A:795 , HOH A:806 , HIS B:437 , PRO B:438	BINDING SITE FOR RESIDUE FAD A 500
02	AC2	SOFTWARE	LYS A:50 , ILE A:172 , ALA A:174 , GLY A:175 , TYR A:176 , ILE A:177 , GLU A:180 , ALA A:196 , LEU A:197 , GLU A:198 , PHE A:228 , ALA A:229 , VAL A:230 , VAL A:260 , GLY A:261 , GLN A:308 , LEU A:309 , VAL A:341 , PHE A:343 , FAD A:500 , HOH A:705 , HOH A:805 , HOH A:840 , HOH A:863	BINDING SITE FOR RESIDUE NAD A 600
03	AC3	SOFTWARE	ARG A:104 , HOH A:819 , SER B:280	BINDING SITE FOR RESIDUE CL A 464
04	AC4	SOFTWARE	ARG A:115	BINDING SITE FOR RESIDUE CL A 465
05	AC5	SOFTWARE	HIS A:120 , HIS A:383 , HOH A:812 , HOH A:857 , HOH A:858 , HOH A:859	BINDING SITE FOR RESIDUE NI A 466
06	AC6	SOFTWARE	HOH A:860	BINDING SITE FOR RESIDUE CL A 467
07	AC7	SOFTWARE	THR A:2 , GLN A:3 , HIS A:4	BINDING SITE FOR RESIDUE NI A 468
08	AC8	SOFTWARE	HIS A:345	BINDING SITE FOR RESIDUE CL A 469
09	AC9	SOFTWARE	HIS A:437 , PRO A:438 , GLY B:11 , GLY B:13 , SER B:14 , GLY B:15 , GLU B:34 , SER B:35 , GLY B:40 , THR B:41 , CYS B:42 , VAL B:45 , GLY B:46 , CYS B:47 , LYS B:50 , GLY B:112 , HIS B:113 , ALA B:114 , ALA B:137 , THR B:138 , GLY B:139 , ARG B:262 , LEU B:269 , GLY B:301 , ASP B:302 , GLN B:308 , LEU B:309 , THR B:310 , PRO B:311 , NAD B:600 , HOH B:686 , HOH B:703 , HOH B:742 , HOH B:750 , HOH B:751 , HOH B:778	BINDING SITE FOR RESIDUE FAD B 500
10	BC1	SOFTWARE	LYS B:50 , ILE B:172 , ALA B:174 , GLY B:175 , TYR B:176 , ILE B:177 , GLU B:180 , ALA B:196 , LEU B:197 , GLU B:198 , PHE B:228 , VAL B:230 , VAL B:260 , GLY B:261 , GLN B:308 , LEU B:309 , VAL B:341 , PHE B:343 , FAD B:500 , HOH B:659 , HOH B:663 , HOH B:743	BINDING SITE FOR RESIDUE NAD B 600
11	BC2	SOFTWARE	SER A:280 , ARG B:104	BINDING SITE FOR RESIDUE CL B 464
12	BC3	SOFTWARE	ARG B:115	BINDING SITE FOR RESIDUE CL B 465
13	BC4	SOFTWARE	HIS B:120 , HIS B:383 , HOH B:800 , HOH B:801 , HOH B:802	BINDING SITE FOR RESIDUE NI B 466
14	BC5	SOFTWARE	THR B:2 , GLN B:3 , HIS B:4	BINDING SITE FOR RESIDUE NI B 468
15	BC6	SOFTWARE	HIS B:345	BINDING SITE FOR RESIDUE CL B 469

Asymmetric/Biological Unit

No.	Residues
1	A:42	-	A:47
2	B:42	-	B:47

Asymmetric/Biological Unit

No.	Residues
1	His A:345	-	Pro A:346
2	His A:437	-	Pro A:438
3	His B:345	-	Pro B:346
4	His B:437	-	Pro B:438

(no "SAP(SNP)/Variant" information available for 2RAB)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRIDINE_REDOX_1	PS00076	Pyridine nucleotide-disulphide oxidoreductases class-I active site.	GASHR_MARGR	39-49	2	A:39-49 B:39-49

(no "Exon" information available for 2RAB)

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:451
 aligned with GASHR_MARGR | D0VWY5 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:454
                                    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    
          GASHR_MARGR     2 TQHFDLIAIGGGSGGLAVAEKAAAFGKRVALIESKALGGTCVNVGCVPKKVMWYASHLAEAVRDAPGFGVQASGGTLDWPRLVAGRDRYIGAINSFWDGYVERLGITRVDGHARFVDAHTIEVEGQRLSADHIVIATGGRPIVPRLPGAELGITSDGFFALQQQPKRVAIIGAGYIGIELAGLLRSFGSEVTVVALEDRLLFQFDPLLSATLAENMHAQGIETHLEFAVAALERDAQGTTLVAQDGTRLEGFDSVIWAVGRAPNTRDLGLEAAGIEVQSNGMVPTDAYQNTNVPGVYALGDITGRDQLTPVAIAAGRRLAERLFDGQSERKLDYDNIPTVVFAHPPLSKVGLSEPEARERLGDVLTVYETSFTPMRYALNEHGPKTAMKLVCAGPEQRVVGVHVIGDGADEMLQGFAVAVKMGATKADFDNTVAIHPGSAEELVTLKEPVRRPG 455
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rabA01 A:2-142,A:261-336  [code=3.50.50.60, no name defined]                                                                                2rabA02 A:143-260  [code=3.50.50.60, no name defined]                                                                 2rabA01 A:2-142,A:261-336  [code=3.50.50.60, no name defined]               2rabA03 A:337-448  [code=3.30.390.30, no name defined]                                                          ------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....--..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeeee..eeee..eeeeeeeeee...eee......hhhhh.hhhhhhhh.....eeeee..hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhh..eeee...eeeeee....eeeee....ee-ee.eeee...eee.....hhhhhh.....................eee.hhhhh...hhhhhhhhhhhhhhhhhh.............eee.....eeeee.hhhhhhhhhh..eeeeeeee.hhhhh.......eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PYRIDINE_RE---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rab A   2 TQHFDLIAIGGGSGGLAVAEKAAAFGKRVALIESKALGGTCVNVGCVPKKVMWYASHLAEAVRDAPGFGVQAS--TLDWPRLVAGRDRYIGAINSFWDGYVERLGITRVDGHARFVDAHTIEVEGQRLSADHIVIATGGRPIVPRLPGAELGITSDGFFALQQQPKRVAIIGAGYIGIELAGLLRSFGSEVTVVALEDRLLFQFDPLLSATLAENMHAQGIETHLEFAVAALERDAQGTTLVAQDGTRL-GFDSVIWAVGRAPNTRDLGLEAAGIEVQSNGMVPTDAYQNTNVPGVYALGDITGRDQLTPVAIAAGRRLAERLFDGQSERKLDYDNIPTVVFAHPPLSKVGLSEPEARERLGDVLTVYETSFTPMRYALNEHGPKTAMKLVCAGPEQRVVGVHVIGDGADEMLQGFAVAVKMGATKADFDNTVAIHPGSAEELVTLKEPVRRPG 455
                                    11        21        31        41        51        61        71  |  |  81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        |-|      261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451    
                                                                                                   74 77                                                                                                                                                                          250 |                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                    252

Chain B from PDB  Type:PROTEIN  Length:452
 aligned with GASHR_MARGR | D0VWY5 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:455
                                    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     
          GASHR_MARGR     2 TQHFDLIAIGGGSGGLAVAEKAAAFGKRVALIESKALGGTCVNVGCVPKKVMWYASHLAEAVRDAPGFGVQASGGTLDWPRLVAGRDRYIGAINSFWDGYVERLGITRVDGHARFVDAHTIEVEGQRLSADHIVIATGGRPIVPRLPGAELGITSDGFFALQQQPKRVAIIGAGYIGIELAGLLRSFGSEVTVVALEDRLLFQFDPLLSATLAENMHAQGIETHLEFAVAALERDAQGTTLVAQDGTRLEGFDSVIWAVGRAPNTRDLGLEAAGIEVQSNGMVPTDAYQNTNVPGVYALGDITGRDQLTPVAIAAGRRLAERLFDGQSERKLDYDNIPTVVFAHPPLSKVGLSEPEARERLGDVLTVYETSFTPMRYALNEHGPKTAMKLVCAGPEQRVVGVHVIGDGADEMLQGFAVAVKMGATKADFDNTVAIHPGSAEELVTLKEPVRRPGD 456
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rabB01 B:2-142,B:261-336  [code=3.50.50.60, no name defined]                                                                                2rabB02 B:143-260  [code=3.50.50.60, no name defined]                                                                 2rabB01 B:2-142,B:261-336  [code=3.50.50.60, no name defined]               2rabB03 B:337-448  [code=3.30.390.30, no name defined]                                                          -------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....--..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeeee..eeee..eeeeeeeeee...eee......hhhhh.hhhhhhhh.....eeeee..hhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhh..eeee...eeeeeee..eeeeee....ee-ee.eeee...eee................................eee.hhhhh...hhhhhhhhhhhhhhhhhh.............eee.....eeeee.hhhhhhhhh...eeeeeeee.hhhhh.......eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------PYRIDINE_RE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rab B   2 TQHFDLIAIGGGSGGLAVAEKAAAFGKRVALIESKALGGTCVNVGCVPKKVMWYASHLAEAVRDAPGFGVQAS--TLDWPRLVAGRDRYIGAINSFWDGYVERLGITRVDGHARFVDAHTIEVEGQRLSADHIVIATGGRPIVPRLPGAELGITSDGFFALQQQPKRVAIIGAGYIGIELAGLLRSFGSEVTVVALEDRLLFQFDPLLSATLAENMHAQGIETHLEFAVAALERDAQGTTLVAQDGTRL-GFDSVIWAVGRAPNTRDLGLEAAGIEVQSNGMVPTDAYQNTNVPGVYALGDITGRDQLTPVAIAAGRRLAERLFDGQSERKLDYDNIPTVVFAHPPLSKVGLSEPEARERLGDVLTVYETSFTPMRYALNEHGPKTAMKLVCAGPEQRVVGVHVIGDGADEMLQGFAVAVKMGATKADFDNTVAIHPGSAEELVTLKEPVRRPGD 456
                                    11        21        31        41        51        61        71  |  |  81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        |-|      261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451     
                                                                                                   74 77                                                                                                                                                                          250 |                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                                    252

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 '\|'

(no "SCOP Domain" information available for 2RAB)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Enolase-like; domain 1 (252)

Homologous Superfamily: [code=3.30.390.30, no name defined] (99)

Marichromatium gracile. Organism_taxid: 1048. (2)

1a	2rabA03	A:337-448
1b	2rabB03	B:337-448

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Marichromatium gracile. Organism_taxid: 1048. (2)

2a	2rabA01	A:2-142,A:261-336
2b	2rabB01	B:2-142,B:261-336
2c	2rabA02	A:143-260
2d	2rabB02	B:143-260

(no "Pfam Domain" information available for 2RAB)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GASHR_MARGR | D0VWY5)

molecular function
	GO:0050661	NADP binding	Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0004362	glutathione-disulfide reductase activity	Catalysis of the reaction: 2 glutathione + NADP+ = glutathione disulfide + NADPH + H+.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0016668	oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
	GO:0045454	cell redox homeostasis	Any process that maintains the redox environment of a cell or compartment within a cell.
	GO:0098869	cellular oxidant detoxification	Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
	GO:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	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:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		His A:345 - Pro A:346	[ RasMol ]
		His A:437 - Pro A:438	[ RasMol ]
		His B:345 - Pro B:346	[ RasMol ]
		His B:437 - Pro B:438	[ RasMol ]

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	2rab
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	GASHR_MARGR \| D0VWY5	:	2r9z

2r9z	NATIVE GAR STRUCTURE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (15, 15)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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