Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  SULFITE REDUCTASE HEMOPROTEIN, OXIDIZED, SIROHEME FEIII [4FE-4S] +2, SULFITE COMPLEX
 
Authors :  B. R. Crane, E. D. Getzoff
Date :  10 Jul 97  (Deposition) - 14 Jan 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Siroheme Feiii, [4Fe-4S], Sulfite Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. R. Crane, L. M. Siegel, E. D. Getzoff
Probing The Catalytic Mechanism Of Sulfite Reductase By X-Ray Crystallography: Structures Of The Escherichia Coli Hemoprotein In Complex With Substrates, Inhibitors, Intermediates, And Products.
Biochemistry V. 36 12120 1997
PubMed-ID: 9315849  |  Reference-DOI: 10.1021/BI971066I
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SULFITE REDUCTASE HEMOPROTEIN
    Chains: A
    EC Number: 1.8.1.2
    Engineered: YES
    Expression System: SALMONELLA TYPHIMURIUM
    Expression System Gene: CYSIJ
    Expression System Plasmid: PJYW613
    Expression System Strain: CYSI68
    Expression System Taxid: 602
    Gene: CYSIJ
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 37762
    Other Details: PBR322 DERIVATIVE CONTAINING ESCHERICHIA COLI CYSIJ AND S. TYPHIMURIUM CYSG UNDER CONTROL OF THE CYSJIH PROMOTOR EXPRESSED IN A S. TYPHIMURIUM CYSI AUXOTROPH
    Strain: B
    Synonym: SIRHP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2SF41Ligand/IonIRON/SULFUR CLUSTER
3SO31Ligand/IonSULFITE ION
4SRM1Ligand/IonSIROHEME

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:83 , ARG A:153 , LYS A:215 , LYS A:217 , SRM A:580 , HOH A:744 , HOH A:800BINDING SITE FOR RESIDUE SO3 A 585
2AC2SOFTWAREILE A:362 , ASN A:395 , GLN A:396 , ASN A:397 , HOH A:833BINDING SITE FOR RESIDUE NA A 590
3AC3SOFTWARECYS A:434 , CYS A:440 , ALA A:443 , THR A:477 , GLY A:478 , CYS A:479 , ASN A:481 , CYS A:483 , SRM A:580BINDING SITE FOR RESIDUE SF4 A 575
4AC4SOFTWARELEU A:81 , ARG A:83 , ARG A:113 , THR A:115 , ASN A:116 , ARG A:117 , THR A:119 , GLN A:121 , HIS A:123 , ARG A:214 , LYS A:215 , LYS A:217 , ALA A:232 , GLY A:256 , LEU A:257 , SER A:258 , GLN A:396 , ALA A:433 , CYS A:434 , VAL A:435 , THR A:439 , CYS A:440 , PRO A:441 , LEU A:442 , ASN A:481 , GLY A:482 , CYS A:483 , ARG A:485 , SF4 A:575 , SO3 A:585 , HOH A:623 , HOH A:630 , HOH A:648 , HOH A:696 , HOH A:716 , HOH A:743 , HOH A:744 , HOH A:811 , HOH A:814 , HOH A:836 , HOH A:929BINDING SITE FOR RESIDUE SRM A 580

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GEP)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:223 -Pro A:224
2Phe A:437 -Pro A:438

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NIR_SIRPS00365 Nitrite and sulfite reductases iron-sulfur/siroheme-binding site.CYSI_ECOLI477-493  1A:477-493

(-) Exons   (0, 0)

(no "Exon" information available for 2GEP)

(-) 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:472
 aligned with CYSI_ECOLI | P17846 from UniProtKB/Swiss-Prot  Length:570

    Alignment length:490
                                    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       460       470       480       490       500       510       520       530       540       550       560       570
           CYSI_ECOLI    81 LLRCRLPGGVITTKQWQAIDKFAGENTIYGSIRLTNRQTFQFHGILKKNVKPVHQMLHSVGLDALATANDMNRNVLCTSNPYESQLHAEAYEWAKKISEHLLPRTRAYAEIWLDQEKVATTDEEPILGQTYLPRKFKTTVVIPPQNDIDLHANDMNFVAIAENGKLVGFNLLVGGGLSIEHGNKKTYARTASEFGYLPLEHTLAVAEAVVTTQRDWGNRTDRKNAKTKYTLERVGVETFKAEVERRAGIKFEPIRPYEFTGRGDRIGWVKGIDDNWHLTLFIENGRILDYPARPLKTGLLEIAKIHKGDFRITANQNLIIAGVPESEKAKIEKIAKESGLMNAVTPQRENSMACVSFPTCPLAMAEAERFLPSFIDNIDNLMAKHGVSDEHIVMRVTGCPNGCGRAMLAEVGLVGKAPGRYNLHLGGNRIGTRIPRMYKENITEPEILASLDELIGRWAKEREAGEGFGDFTVRAGIIRPVLDPARDLWD 570
               SCOP domains d2gepa1 A:81-145 Sulfite reductase, domains 1 and 3              d2gepa3 A:146-345 Sulfite reductase hemo                  protein (SiRHP), domains 2 and 4                                                                                                              d2gepa2 A:346-425 Sulfite reductase, domains 1 and 3                            d2gepa4 A:426-570 Sulfite reductase hemoprotein (SiRHP), domains 2 and 4                                                                          SCOP domains
               CATH domains 2gepA02 A:81-145,A:341-424 Sulfite Reductase Hemoprotein;Domain 2---2gepA01 A:149-340 Sulfite Reductase H                  emoprotein, domain 1                                                                                                                     2gepA02 A:81-145,A:341-424 Sulfite Reductase Hemoprotein;Domain 2                   2gepA03 A:425-567 Sulfite Reductase Hemoprotein, domain 1                                                                                      --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author eeeee...eee.hhhhhhhhhhhhhh....eeeee...eeeeeeee..hhhhhhhhhhhh..............eeee.......hhhhhhhhhhhhhhhhhh..------------------...........eeeeeee.......hhhhheeeeeeeee..eeeeeeeeee.................eeeeeeee.hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh..................eeeee..eeeeeeee...eee.......hhhhhhhhhhhh..eeeee...eeeeeeee..hhhhhhhhhhhh.......hhhhheeee...............hhhhhhhhhhhhhhhh.......eeee........hhhhheeeeeeee..eeeeeee.........eeeeeeeehhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NIR_SIR          ----------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gep A  81 LLRCRLPGGVITTKQWQAIDKFAGENTIYGSIRLTNRQTFQFHGILKKNVKPVHQMLHSVGLDALATANDMNRNVLCTSNPYESQLHAEAYEWAKKISEHLLPRT------------------EPILGQTYLPRKFKTTVVIPPQNDIDLHANDMNFVAIAENGKLVGFNLLVGGGLSIEHGNKKTYARTASEFGYLPLEHTLAVAEAVVTTQRDWGNRTDRKNAKTKYTLERVGVETFKAEVERRAGIKFEPIRPYEFTGRGDRIGWVKGIDDNWHLTLFIENGRILDYPARPLKTGLLEIAKIHKGDFRITANQNLIIAGVPESEKAKIEKIAKESGLMNAVTPQRENSMACVSFPTCPLAMAEAERFLPSFIDNIDNLMAKHGVSDEHIVMRVTGCPNGCGRAMLAEVGLVGKAPGRYNLHLGGNRIGTRIPRMYKENITEPEILASLDELIGRWAKEREAGEGFGDFTVRAGIIRPVLDPARDLWD 570
                                    90       100       110       120       130       140       150       160       170       180    |    -         -   |   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       460       470       480       490       500       510       520       530       540       550       560       570
                                                                                                                                  185                204
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CYSI_ECOLI | P17846)
molecular function
    GO:0051539    4 iron, 4 sulfur cluster binding    Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
    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:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004783    sulfite reductase (NADPH) activity    Catalysis of the reaction: hydrogen sulfide + 3 NADP+ + 3 H2O = sulfite + 3 NADPH + 3 H+.
    GO:0050311    sulfite reductase (ferredoxin) activity    Catalysis of the reaction: hydrogen sulfide + 3 oxidized ferredoxin + 3 H2O = sulfite + 3 reduced ferredoxin.
    GO:0016002    sulfite reductase activity    Catalysis of the reaction: hydrogen sulfide + acceptor + 3 H2O = sulfite + reduced acceptor.
biological process
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0019344    cysteine biosynthetic process    The chemical reactions and pathways resulting in the formation of cysteine, 2-amino-3-mercaptopropanoic acid.
    GO:0070814    hydrogen sulfide biosynthetic process    The chemical reactions and pathways resulting in the formation of hydrogen sulfide, H2S.
    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.
    GO:0000103    sulfate assimilation    The pathways by which inorganic sulfate is processed and incorporated into sulfated compounds.
    GO:0019419    sulfate reduction    The chemical reactions and pathways resulting in the reduction of sulfate to another sulfur-containing ion or compound such as hydrogen sulfide, adenosine-phosphosulfate (APS) or thiosulfate.
cellular component
    GO:0009337    sulfite reductase complex (NADPH)    A multisubunit iron flavoprotein, which in yeast is composed of 2 alpha and 2 beta subunits. Catalyzes the reduction of sulfite to sulfide.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SF4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SRM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:437 - Pro A:438   [ RasMol ]  
    Pro A:223 - Pro A:224   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2gep
    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
  CYSI_ECOLI | P17846
    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)
  1.8.1.2
    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

(-) Analysis Tools

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
  CYSI_ECOLI | P17846
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CYSI_ECOLI | P17846: 1aop 2aop 3aop 3geo 4aop 4g38 4g39 4gep 4htr 5aop 5gep 6gep 7gep 8gep

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GEP)