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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FLAVODIIRON PROTEIN FROM GIARDIA INTESTINALIS
 
Authors :  A. Di Matteo, F. M. Scandurra, F. Testa, E. Forte, P. Sarti, M. Brunori, A. Giuffre
Date :  14 Jun 07  (Deposition) - 11 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Flavodoxin Like, Beta Lactamase Like, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Di Matteo, F. M. Scandurra, F. Testa, E. Forte, P. Sarti, M. Brunori, A. Giuffre
The O2-Scavenging Flavodiiron Protein In The Human Parasite Giardia Intestinalis
J. Biol. Chem. V. 283 4061 2008
PubMed-ID: 18077462  |  Reference-DOI: 10.1074/JBC.M705605200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - A-TYPE FLAVOPROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: DH5ALPHA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FPRA
    Organism Scientific: GIARDIA INTESTINALIS
    Organism Taxid: 5741
    Other Details: SYNONYM GIARDIA INTESTINALIS
    Strain: WB C6
    Synonym: FLAVODIIRON PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1FEO2Ligand/IonMU-OXO-DIIRON
2FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
3NO35Ligand/IonNITRATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1FEO4Ligand/IonMU-OXO-DIIRON
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
3NO310Ligand/IonNITRATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:30 , HIS A:31 , GLU A:87 , ASP A:89 , HIS A:152 , ASP A:171 , HIS A:176 , TYR A:199 , ILE A:203 , HIS A:230 , FEO A:701BINDING SITE FOR RESIDUE NO3 A 501
2AC2SOFTWAREGLY A:32 , ASP A:264 , ILE A:298 , MET A:323 , PRO A:324 , SER A:325 , HOH A:1073 , HOH A:1089 , HOH A:1357BINDING SITE FOR RESIDUE NO3 A 502
3AC3SOFTWAREARG A:282 , HOH A:1389 , GLU B:12 , MET B:13 , HOH B:1032BINDING SITE FOR RESIDUE NO3 A 503
4AC4SOFTWAREHIS B:31 , GLU B:87 , ASP B:89 , HIS B:152 , ASP B:171 , HIS B:176 , TYR B:199 , HIS B:230 , FEO B:701BINDING SITE FOR RESIDUE NO3 B 501
5AC5SOFTWAREGLY B:32 , ASP B:264 , ILE B:298 , MET B:323 , PRO B:324 , SER B:325 , HOH B:1102 , HOH B:1218 , HOH B:1271 , HOH B:1278BINDING SITE FOR RESIDUE NO3 B 502
6AC6SOFTWAREGLU A:87 , TRP A:153 , SER A:265 , MET A:266 , TYR A:267 , GLY A:268 , THR A:269 , THR A:270 , PRO A:316 , THR A:317 , LEU A:318 , ASN A:319 , ASN A:320 , ALA A:349 , PHE A:350 , GLY A:351 , TRP A:352 , SER A:353 , PHE A:382 , HOH A:1077 , HOH A:1113 , HOH A:1126 , HOH A:1206 , HOH A:1242BINDING SITE FOR RESIDUE FMN A 601
7AC7SOFTWAREHIS A:85 , GLU A:87 , ASP A:89 , HIS A:90 , HIS A:152 , ASP A:171 , HIS A:230 , NO3 A:501BINDING SITE FOR RESIDUE FEO A 701
8AC8SOFTWAREGLU B:87 , TRP B:153 , SER B:265 , MET B:266 , TYR B:267 , GLY B:268 , THR B:269 , THR B:270 , PRO B:316 , THR B:317 , LEU B:318 , ASN B:319 , ASN B:320 , ALA B:349 , PHE B:350 , GLY B:351 , TRP B:352 , SER B:353 , PHE B:382 , HOH B:1050 , HOH B:1115 , HOH B:1119 , HOH B:1122 , HOH B:1257BINDING SITE FOR RESIDUE FMN B 601
9AC9SOFTWAREHIS B:85 , GLU B:87 , ASP B:89 , HIS B:90 , HIS B:152 , ASP B:171 , HIS B:230 , NO3 B:501BINDING SITE FOR RESIDUE FEO B 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q9U)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:151 -His A:152
2Leu B:151 -His B:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Q9U)

(-) Exons   (0, 0)

(no "Exon" information available for 2Q9U)

(-) 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:409
 aligned with Q86QZ1_GIAIN | Q86QZ1 from UniProtKB/TrEMBL  Length:414

    Alignment length:409
                                    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         
         Q86QZ1_GIAIN     4 KPKYVQDQEMIPGVYWVGIVDWMVRIFHGYHTDEGSSYNSYFIDDECPTVIDSVKYPFAEEWLSRIAACCPLDKIKYVVMNHAEGDHASSLKDHYHKFTNATFVCTKKCQEHLKILYGMEKATWLIVDDKYTLKIGKRTLKFIPVPLLHWPDSTFTYCPEDKILFSNDGFGQHYATSRRWADECDVSHVMHLFKEYTANILGLFSAQMRKALEVASTVEIKYILSAHGVSWRGDAMGLAIAEYDRWSKGQHCQKKVTVVLDSMYGTTHRMALALLDGARSTGCETVLLEMTSSDITKVALHTYDSGAVAFASPTLNNTMMPSVAAALNYVRGLTLIKGKPAFAFGAFGWSNRAVPDIVAELRDGCKADVYDEKGITFKFNYTEELLEQAYNAGVDLGKRAIAYCEKNAP 412
               SCOP domains d2q9ua1 A:4-253 Nitric oxide reductase N-terminal domain                                                                                                                                                                                                  d2q9ua2 A:254-412 Nitric oxide reductase C-terminal domain                                                                                                      SCOP domains
               CATH domains 2q9uA01 A:4-251 Metallo-beta-lactamase, chain A                                                                                                                                                                                                         ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eee..eee....ee..ee....eee..eee.....eee...hhhhhhhhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhh.....eee......ee....eeeeee.........eeeee....eeeee............hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh....eeee.....eehhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhh..........eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q9u A   4 KPKYVQDQEMIPGVYWVGIVDWMVRIFHGYHTDEGSSYNSYFIDDECPTVIDSVKYPFAEEWLSRIAACCPLDKIKYVVMNHAEGDHASSLKDHYHKFTNATFVCTKKCQEHLKILYGMEKATWLIVDDKYTLKIGKRTLKFIPVPLLHWPDSTFTYCPEDKILFSNDGFGQHYATSRRWADECDVSHVMHLFKEYTANILGLFSAQMRKALEVASTVEIKYILSAHGVSWRGDAMGLAIAEYDRWSKGQHCQKKVTVVLDSMYGTTHRMALALLDGARSTGCETVLLEMTSSDITKVALHTYDSGAVAFASPTLNNTMMPSVAAALNYVRGLTLIKGKPAFAFGAFGWSNRAVPDIVAELRDGCKADVYDEKGITFKFNYTEELLEQAYNAGVDLGKRAIAYCEKNAP 412
                                    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         


Chain B from PDB  Type:PROTEIN  Length:407
 aligned with Q86QZ1_GIAIN | Q86QZ1 from UniProtKB/TrEMBL  Length:414

    Alignment length:407
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       
         Q86QZ1_GIAIN     6 KYVQDQEMIPGVYWVGIVDWMVRIFHGYHTDEGSSYNSYFIDDECPTVIDSVKYPFAEEWLSRIAACCPLDKIKYVVMNHAEGDHASSLKDHYHKFTNATFVCTKKCQEHLKILYGMEKATWLIVDDKYTLKIGKRTLKFIPVPLLHWPDSTFTYCPEDKILFSNDGFGQHYATSRRWADECDVSHVMHLFKEYTANILGLFSAQMRKALEVASTVEIKYILSAHGVSWRGDAMGLAIAEYDRWSKGQHCQKKVTVVLDSMYGTTHRMALALLDGARSTGCETVLLEMTSSDITKVALHTYDSGAVAFASPTLNNTMMPSVAAALNYVRGLTLIKGKPAFAFGAFGWSNRAVPDIVAELRDGCKADVYDEKGITFKFNYTEELLEQAYNAGVDLGKRAIAYCEKNAP 412
               SCOP domains d2q9ub1 B:6-253 Nitric oxide reductase N-terminal domain                                                                                                                                                                                                d2q9ub2 B:254-412 Nitric oxide reductase C-terminal domain                                                                                                      SCOP domains
               CATH domains 2q9uB01 B:6-251 Metallo-beta-lactamase, chain A                                                                                                                                                                                                       ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------Lactamase_B-2q9uB01 B:36-230                                                                                                                                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------Lactamase_B-2q9uB02 B:36-230                                                                                                                                                                       -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ......eee..eee..eee....ee..ee....eee..eee.....eee...hhhhhhhhhhhhhhhhhhhhh.eee....hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhh....eeee......ee....eeeeee.........eeeee....eeeee............hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeee.....eehhhhhhhhhhhhhhhh......eeeeee....hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.eeeee..ee..eehhhhhhhhhhhhhhh......eeeeeee....hhhhhhhhhhhhh..........eeee...hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q9u B   6 KYVQDQEMIPGVYWVGIVDWMVRIFHGYHTDEGSSYNSYFIDDECPTVIDSVKYPFAEEWLSRIAACCPLDKIKYVVMNHAEGDHASSLKDHYHKFTNATFVCTKKCQEHLKILYGMEKATWLIVDDKYTLKIGKRTLKFIPVPLLHWPDSTFTYCPEDKILFSNDGFGQHYATSRRWADECDVSHVMHLFKEYTANILGLFSAQMRKALEVASTVEIKYILSAHGVSWRGDAMGLAIAEYDRWSKGQHCQKKVTVVLDSMYGTTHRMALALLDGARSTGCETVLLEMTSSDITKVALHTYDSGAVAFASPTLNNTMMPSVAAALNYVRGLTLIKGKPAFAFGAFGWSNRAVPDIVAELRDGCKADVYDEKGITFKFNYTEELLEQAYNAGVDLGKRAIAYCEKNAP 412
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405
   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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q86QZ1_GIAIN | Q86QZ1)
molecular function
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    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: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.
biological process
    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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