1JOA - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   NADH PEROXIDASE WITH CYSTEINE-SULFENIC ACID

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

Date :   02 Jul 96 (Deposition) - 11 Jan 97 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Oxidoreductase, Cysteine-Sulfenic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. I. Yeh, A. Claiborne, W. G. Hol
Structure Of The Native Cysteine-Sulfenic Acid Redox Center Of Enterococcal Nadh Peroxidase Refined At 2. 8 A Resolution
Biochemistry V. 35 9951 1996
PubMed-ID: 8756456 | Reference-DOI: 10.1021/BI961037S

Molecule 1 - NADH PEROXIDASE
	Chains	:	A
	EC Number	:	1.11.1.1
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	1351
	Other Details	:	ACTIVE, NATIVE FORM WITH CYSTEINE-SULFENIC ACID

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

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

Biological Unit 1 (2, 2)

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

Biological Unit 2 (2, 4)

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

Asymmetric Unit (2, 2)

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 , CSO 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 , ILE A:160 , ASN A:247 , GLY A:280 , ASP A:281 , ALA A:297 , LEU A:298 , ALA A:299 , PHE A:424 , HOH A:504 , HOH A:661 , HOH A:668	BINDING SITE FOR RESIDUE FAD A 448
2	ACT	UNKNOWN	CSO A:42 , HIS A:10 , ARG A:303 , TYR A:159 , FAD A:448	CSO 42 IS THE NATIVE, ACTIVE CYSTEINE-SULFENIC ACID (SOH).

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

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

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

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

(no "Exon" information available for 1JOA)

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
	(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: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 d1joaa1 A:1-119,A:243-321 NADH peroxidase                                                                              d1joaa2 A:120-242 NADH peroxidase                                                                                          d1joaa1 A:1-119,A:243-321 NADH peroxidase                                      d1joaa3 A:322-447 NADH peroxidase                                                                                              SCOP domains
               CATH domains 1joaA01 A:1-33,A:60-112,A:246-326-------1joaA02           -1joaA01 A:1-33,A:60-112,A:246-326                    1joaA02 A:41-58,A:113-244  [code=3.50.50.60, no name defined]                                                                       -1joaA01 A:1-33,A:60-112,A:246-326  [code=3.50.50.60, no name defined]            -------1joaA03 A:334-446  [code=3.30.390.30, no name defined]                                                           - CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox-1joaA01 A:151-232                                                       ----------------------------------------------------------------------------------------------Pyr_redox_dim-1joaA04 A:327-433                                                                            -------------- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox_2-1joaA02 A:190-287                                                                     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Pyr_redox_2-1joaA03 A:190-287                                                                     ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author .eeeee...hhhhhhhhhhhhh....eeeee............hhhhh......hhh.....hhhhhhh.eeee..eeeeeee....eeeeee.....eeeee..eeee...eee............eee..hhhhhhhhhhhhh.....eeeee...hhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhh.eeeee...eeeee......eeee...eee..eeee...eee..hhh........................eee.hhh..eeehhh.eee....hhhhhhhhhhhhh...............eeeee..eeeeeee..hhhhhhh....eeeeeeee..........eeeeeeee......eeeeeeee....hhhhhhhhhhhh....hhhhh...............hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1joa A   1 MKVIVLGSSHGGYEAVEELLNLHPDAEIQWYEKGDFISFLScGMQLYLEGKVKDVNSVRYMTGEKMESRGVNVFSNTEITAIQPKEHQVTVKDLVSGEERVENYDKLIISPGAVPFELDIPGKDLDNIYLMRGRQWAIKLKQKTVDPEVNNVVVIGSGYIGIEAAEAFAKAGKKVTVIDILDRPLGVYLDKEFTDVLTEEMEANNITIATGETVERYEGDGRVQKVVTDKNAYDADLVVVAVGVRPNTAWLKGTLELHPNGLIKTDEYMRTSEPDVFAVGDATLIKYNPADTEVNIALATNARKQGRFAVKNLEEPVKPFPGVQGSSGLAVFDYKFASTGINEVMAQKLGKETKAVTVVEDYLMDFNPDKQKAWFKLVYDPETTQILGAQLMSKADLTANINAISLAIQAKMTIEDLAYADFFFQPAFDKPWNIINTAALEAVKQER 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-CSO

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 (7)

1joaA03

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 (7)

2a	1joaA01	A:1-33,A:60-112,A:246-326
2b	1joaA02	A:41-58,A:113-244

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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CSO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FAD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		ACT	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1joa)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1joa
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NAPE_ENTFA \| P37062
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	1.11.1.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NAPE_ENTFA \| P37062
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	NAPE_ENTFA \| P37062	:	1f8w 1nhp 1nhq 1nhr 1nhs 1npx 2npx

(no "Related Entries Specified in the PDB File" available for 1JOA)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (2, 3)

Pfam Domains (3, 4)

Gene Ontology (8, 8)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File