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(-) Description

Title :  CRYSTAL STRUCTURE OF NITRITE REDUCTASE FROM PSEUDOALTEROMONAS HALOPLANKTIS TAC125
 
Authors :  M. Nojiri, A. Tsuda, K. Yamaguchi, S. Suzuki
Date :  27 May 08  (Deposition) - 09 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Nitrite, Electron Transfer, Electron Transport, Heme, Iron, Metal- Binding, Oxidoreductase, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nojiri, H. Koteishi, A. Tsuda, T. Nakagami, K. Kobayashi, T. Inoue, K. Yamaguchi, S. Suzuki
Electron Transfer Processes Within And Between Proteins Containing The Heme C And Blue Cu
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE NITRITE REDUCTASE
    Chains: A
    EC Number: 1.7.99.3, 1.7.2.1
    Fragment: UNP RESIDUES 26-467
    Organism Scientific: PSEUDOALTEROMONAS HALOPLANKTIS
    Organism Taxid: 326442
    Strain: TAC125

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
1CU2Ligand/IonCOPPER (II) ION
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO43Ligand/IonSULFATE ION
4SUC1Ligand/IonSUCROSE
Biological Unit 1 (3, 15)
No.NameCountTypeFull Name
1CU-1Ligand/IonCOPPER (II) ION
2HEM3Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
3SO49Ligand/IonSULFATE ION
4SUC3Ligand/IonSUCROSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:99 , SER A:100 , SER A:101 , PHE A:102 , THR A:103 , ALA A:104 , HIS A:107 , THR A:108 , SER A:109 , ASN A:333 , ASN A:334 , GLU A:337 , PRO A:362 , HOH A:862 , HOH A:1036 , HOH A:1039 , HOH A:1071 , HOH A:1127BINDING SITE FOR RESIDUE SUC A 700
2AC2SOFTWAREHIS A:84 , CYS A:125 , HIS A:133 , MET A:138BINDING SITE FOR RESIDUE CU A 500
3AC3SOFTWAREHIS A:89 , HIS A:124 , HIS A:279 , HOH A:1201BINDING SITE FOR RESIDUE CU A 501
4AC4SOFTWARESER A:26 , ARG A:65 , LYS A:147 , HOH A:1053BINDING SITE FOR RESIDUE SO4 A 801
5AC5SOFTWARELYS A:307 , ASN A:334 , LYS A:335 , LYS A:431 , HOH A:876 , HOH A:1095BINDING SITE FOR RESIDUE SO4 A 802
6AC6SOFTWAREGLU A:34 , ARG A:41 , ASP A:44 , GLY A:45 , HOH A:892 , HOH A:954BINDING SITE FOR RESIDUE SO4 A 803
7AC7SOFTWAREASN A:349 , CYS A:350 , CYS A:353 , HIS A:354 , PRO A:366 , PRO A:367 , LEU A:368 , SER A:371 , TYR A:373 , LEU A:389 , SER A:390 , GLY A:391 , ILE A:393 , TYR A:400 , ASN A:401 , GLY A:402 , MET A:404 , LEU A:409BINDING SITE FOR RESIDUE HEM A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Pro A:14 -Pro A:15
2Val A:57 -Pro A:58
3Ala A:128 -Pro A:129
4Gly A:222 -Pro A:223

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZOO)

(-) Exons   (0, 0)

(no "Exon" information available for 2ZOO)

(-) Sequences/Alignments

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:438
 aligned with Q3IGF7_PSEHT | Q3IGF7 from UniProtKB/TrEMBL  Length:467

    Alignment length:438
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458        
         Q3IGF7_PSEHT    29 LKTEQAILTPPPMVPPAINRDHSAKVVINLETREQVGRIADGVEYVFWSFGETVPGSFIRVREGDEIEFNLSNHPSSKMPHNIDLHAVTGPGGGAESSFTAPGHTSTFNFKALNPGLYIYHCATAPVGMHIANGMYGLILVEPKEGLAPVDREYYLVQGDFYTKGEFGEAGLQPFDMAKAIDEDADYVVFNGSVGSTTDENSLTAKVGETVRLYIGNGGPNLVSSFHVIGEIFDTVYVEGGSLKNHNVQTTLIPAGGAAIVEFKVEVPGTFILVDHSIFRAFNKGALAMLKVEGPDDHSIFTGKTAENVYLPEGSAIQSLDNTFTKITANNKDEQIRFGQRVYEANCMACHQANGEGIPGAFPPLAKSDYLNNNPLLGVNAIIKGLSGPIKVNNVNYNGVMPAMNLNDEDIANVITFVLNNWDNAGGKVSAEQVAKQR 466
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------Cu-oxidase_3-2zooA02 A:34-149                                                                                       -----Cu-oxidase-2zooA01 A:155-298                                                                                                                    --------------------------------------Cytochrome_CBB3-2zooA03 A:337-421                                                    -------------------- Pfam domains
         Sec.struct. author ..eee...................eeeeeeeeeeeeeeee..eeeeeeee........eeee...eeeeeeee..........ee....hhhhhhhhh......eeeeeee....eeeeee....hhhhhhhh..eeeeeee.........eeeeeeeeee.........eee..hhhhhhh....eeee.......hhhhheeee...eeeeeeeeee....eeeeee.....eee.hhh..ee....eeee...eeeeeeee....eeeeeee..hhhhhh...eeeeeee.....................................hhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhee..eee..eee..ee.....hhhhhhhhhhhhhh.........hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zoo A   4 LKTEQAILTPPPMVPPAINRDHSAKVVINLETREQVGRIADGVEYVFWSFGETVPGSFIRVREGDEIEFNLSNHPSSKMPHNIDLHAVTGPGGGAESSFTAPGHTSTFNFKALNPGLYIYHCATAPVGMHIANGMYGLILVEPKEGLAPVDREYYLVQGDFYTKGEFGEAGLQPFDMAKAIDEDADYVVFNGSVGSTTDENSLTAKVGETVRLYIGNGGPNLVSSFHVIGEIFDTVYVEGGSLKNHNVQTTLIPAGGAAIVEFKVEVPGTFILVDHSIFRAFNKGALAMLKVEGPDDHSIFTGKTAENVYLPEGSAIQSLDNTFTKITANNKDEQIRFGQRVYEANCMACHQANGEGIPGAFPPLAKSDYLNNNPLLGVNAIIKGLSGPIKVNNVNYNGVMPAMNLNDEDIANVITFVLNNWDNAGGKVSAEQVAKQR 441
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2ZOO)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: CU_oxidase (192)
(-)
Clan: Cytochrome-c (108)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q3IGF7_PSEHT | Q3IGF7)
molecular function
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0050421    nitrite reductase (NO-forming) activity    Catalysis of the reaction: nitric oxide + H2O + ferricytochrome c = nitrite + ferrocytochrome c + 2 H+.
    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.
biological process
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
    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.

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