1F8W - JenaLib

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Title :   CRYSTAL STRUCTURE OF NADH PEROXIDASE MUTANT: R303M

Authors :   J. I. Yeh, A. Claiborne, W. G. J. Hol

Date :   05 Jul 00 (Deposition) - 05 Feb 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)
Biol. Unit 2: A  (2x)

Keywords :   Interface, Fad, Nad-Binding Domains, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. J. Crane 3Rd. , J. I. Yeh, J. Luba, A. Claiborne
Analysis Of The Kinetic And Redox Properties Of The Nadh Peroxidase R303M Mutant: Correlation With The Crystal Structure.
Biochemistry V. 39 10353 2000
PubMed-ID: 10956025 | Reference-DOI: 10.1021/BI000553M
(for further references see the PDB file header)

Molecule 1 - NADH PEROXIDASE
	Chains	:	A
	EC Number	:	1.11.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PR303M
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	1351

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CSX	1	Mod. Amino Acid	S-OXY CYSTEINE
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CSX	4	Mod. Amino Acid	S-OXY CYSTEINE
2	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CSX	2	Mod. Amino Acid	S-OXY CYSTEINE
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:6 , GLY A:7 , SER A:9 , HIS A:10 , GLY A:11 , GLU A:32 , LYS A:33 , SER A:41 , CSX A:42 , THR A:77 , GLU A:78 , ILE A:79 , SER A:110 , PRO A:111 , GLY A:112 , ALA A:113 , MET A:131 , ARG A:132 , TYR A:159 , ASN A:247 , GLY A:280 , ASP A:281 , ALA A:297 , LEU A:298 , ALA A:299 , THR A:300 , PHE A:424 , GLN A:425 , HOH A:451 , HOH A:492 , HOH A:506 , HOH A:567	BINDING SITE FOR RESIDUE FAD A 448

(no "SS Bond" information available for 1F8W)

(no "Cis Peptide Bond" information available for 1F8W)

(no "SAP(SNP)/Variant" information available for 1F8W)

(no "PROSITE Motif" information available for 1F8W)

(no "Exon" information available for 1F8W)

Asymmetric 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
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Chain A from PDB  Type:PROTEIN  Length:447
 aligned with NAPE_ENTFA | P37062 from UniProtKB/Swiss-Prot  Length:447

    Alignment length:447
                                    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       
           NAPE_ENTFA     1 MKVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFISFLSCGMQLYLEGKVKDVNSVRYMTGEKMESRGVNVFSNTEITAIQPKEHQVTVKDLVSGEERVENYDKLIISPGAVPFELDIPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVIGSGYIGIEAAEAFAKAGKKVTVIDILDRPLGVYLDKEFTDVLTEEMEANNITIATGETVERYEGDGRVQKIVTDKNAYDADLVVVAVGVRPNTAWLKGTLELHPNGLIKTDEYMRTSEPDVFAVGDATLIKYNPADTEVNIALATNARKQGRFAVKNLEEPVKPFPGVQGSSGLAVFDYKFASTGINEVMAQKLGKETKAVTVVEDYLMDFNPDKQKAWFKLVYDPETTQILGAQLMSKADLTANINAISLAIQAKMTIEDLAYADFFFQPAFDKPWNIINTAALEAVKQER 447
               SCOP domains d1f8wa1 A:1-119,A:243-321 NADH peroxidase                                                                              d1f8wa2 A:120-242 NADH peroxidase                                                                                          d1f8wa1 A:1-119,A:243-321 NADH peroxidase                                      d1f8wa3 A:322-447 NADH peroxidase                                                                                              SCOP domains
               CATH domains 1f8wA01 A:1-33,A:60-112,A:246-326-------1f8wA02           -1f8wA01 A:1-33,A:60-112,A:246-326                    1f8wA02 A:41-58,A:113-244  [code=3.50.50.60, no name defined]                                                                       -1f8wA01 A:1-33,A:60-112,A:246-326  [code=3.50.50.60, no name defined]            -------1f8wA03 A:334-446  [code=3.30.390.30, no name defined]                                                           - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh...eeeee........hhhhhhhhhh....hhhhh...hhhhhhh..eeee..eeeeeee....eeeeee.....eeeee..eeee...eee............ee..hhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhh..eeee....eeeee......eeee...eee..eeee...eee.hhhh........................eee......eeehhhheee...hhhhhhhhhhhhhhh..............eeeee..eeeeeee.hhhhhhhhh...eeeeeeee..........eeeeeeee......eeeeeeee.....hhhhhhhhhhhh..hhhhhhh.............hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f8w A   1 MKVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFISFLScGMQLYLEGKVKDVNSVRYMTGEKMESRGVNVFSNTEITAIQPKEHQVTVKDLVSGEERVENYDKLIISPGAVPFELDIPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVIGSGYIGIEAAEAFAKAGKKVTVIDILDRPLGVYLDKEFTDVLTEEMEANNITIATGETVERYEGDGRVQKVVTDKNAYDADLVVVAVGVRPNTAWLKGTLELHPNGLIKTDEYMRTSEPDVFAVGDATLIKYNPADTEVNIALATNAMKQGRFAVKNLEEPVKPFPGVQGSSGLAVFDYKFASTGINEVMAQKLGKETKAVTVVEDYLMDFNPDKQKAWFKLVYDPETTQILGAQLMSKADLTANINAISLAIQAKMTIEDLAYADFFFQPAFDKPWNIINTAALEAVKQER 447
                                    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       
                                                                    42-CSX

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 '\|'

Asymmetric 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)

Enterococcus faecalis. Organism_taxid: 1351. (1)

1f8wA03

A:334-446

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

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

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

Enterococcus faecalis. Organism_taxid: 1351. (1)

2a	1f8wA01	A:1-33,A:60-112,A:246-326
2b	1f8wA02	A:41-58,A:113-244

(no "Pfam Domain" information available for 1F8W)

Asymmetric Unit(hide GO term definitions)

Chain A (NAPE_ENTFA | P37062)

molecular function
	GO:0016692	NADH peroxidase activity	Catalysis of the reaction: H(2)O(2) + H(+) + NADH = 2 H(2)O + NAD(+).
	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: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:0004601	peroxidase activity	Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
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: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.

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	1.11.1.1
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	NAPE_ENTFA \| P37062	:	1joa 1nhp 1nhq 1nhr 1nhs 1npx 2npx

1joa	ACTIVE, NATIVE FORM WITH CYSTEINE-SULFENIC ACID
1nhp	NADH PEROXIDASE (NPX) (E.C. 1.11.1.1) MUTANT WITH CYS 42 REPLACED BY ALA (C42A)
1nhq	NADH PEROXIDASE (NPX) (E.C. 1.11.1.1) MUTANT WITH CYS 42 REPLACED BY SER (C42S)
1nhr	NADH PEROXIDASE (NPX) (E.C. 1.11.1.1) MUTANT WITH LEU 40 REPLACED BY CYS (L40C)
1nhs	NADH PEROXIDASE (NPX) (E.C. 1.11.1.1) MUTANT WITH SER 41 REPLACED BY CYS (S41C)
1npx	NADH PEROXIDASE (E.C. 1.11.1.1) NON-ACTIVE FORM WITH CYS 42 OXIDIZED TO A SULFONIC ACID

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