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(-) Description

Title :  CRYSTAL STRUCTURE OF INTACT AHPF
 
Authors :  Z. A. Wood, L. B. Poole, P. A. Karplus
Date :  22 Jan 01  (Deposition) - 14 Feb 01  (Release) - 09 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Thiol-Thiolate Hydrogen Bond, Nucleotide Binding Fold, Thioredoxin Reductase, Thioredoxin, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. A. Wood, L. B. Poole, P. A. Karplus
Structure Of Intact Ahpf Reveals A Mirrored Thioredoxin-Lik Active Site And Implies Large Domain Rotations During Catalysis.
Biochemistry V. 40 3900 2001
PubMed-ID: 11300769  |  Reference-DOI: 10.1021/BI002765P

(-) Compounds

Molecule 1 - ALKYL HYDROPEROXIDE REDUCTASE SUBUNIT F
    Chains: A
    EC Number: 1.8.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: AHPF

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:430 , ARG A:432BINDING SITE FOR RESIDUE SO4 A 800
2AC2SOFTWARELYS A:179 , ILE A:437 , HIS A:438 , SER A:439BINDING SITE FOR RESIDUE SO4 A 801
3AC3SOFTWAREASN A:257 , HIS A:347 , CYS A:348 , GLN A:496 , FAD A:700BINDING SITE FOR RESIDUE CL A 900
4AC4SOFTWAREGLY A:219 , GLY A:221 , PRO A:222 , ALA A:223 , GLU A:243 , ARG A:244 , GLY A:247 , GLN A:248 , ASN A:257 , GLN A:288 , SER A:289 , ALA A:290 , ALA A:321 , THR A:322 , GLY A:323 , CYS A:345 , GLY A:487 , ASP A:488 , LYS A:495 , GLN A:496 , ILE A:497 , ALA A:500 , CL A:900 , HOH A:905 , HOH A:907 , HOH A:909 , HOH A:910 , HOH A:913 , HOH A:925 , HOH A:940 , HOH A:956 , HOH A:987 , HOH A:1071BINDING SITE FOR RESIDUE FAD A 700

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:345 -A:348

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:62 -Pro A:63
2Val A:171 -Pro A:172

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.AHPF_SALTY109-208  1A:109-208
2PYRIDINE_REDOX_2PS00573 Pyridine nucleotide-disulphide oxidoreductases class-II active site.AHPF_SALTY345-365  1A:345-365
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GLUTAREDOXIN_2PS51354 Glutaredoxin domain profile.AHPF_SALTY109-208  2A:109-208
2PYRIDINE_REDOX_2PS00573 Pyridine nucleotide-disulphide oxidoreductases class-II active site.AHPF_SALTY345-365  2A:345-365

(-) Exons   (0, 0)

(no "Exon" information available for 1HYU)

(-) 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:521
 aligned with AHPF_SALTY | P19480 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:521
                                    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       450       460       470       480       490       500       510       520 
           AHPF_SALTY     1 MLDTNMKTQLRAYLEKLTKPVELIATLDDSAKSAEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNPGSQQGPRFAGSPLGHEFTSLVLALLWTGGHPSKEAQSLLEQIRDIDGDFEFETYYSLSCHNCPDVVQALNLMAVLNPRIKHTAIDGGTFQNEITERNVMGVPAVFVNGKEFGQGRMTLTEIVAKVDTGAEKRAAEALNKRDAYDVLIVGSGPAGAAAAVYSARKGIRTGLMGERFGGQVLDTVDIENYISVPKTEGQKLAGALKAHVSDYDVDVIDSQSASKLVPAATEGGLHQIETASGAVLKARSIIIATGAKWRNMNVPGEDQYRTKGVTYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVEHVTLLEFAPEMKADQVLQDKVRSLKNVDIILNAQTTEVKGDGSKVVGLEYRDRVSGDIHSVALAGIFVQIGLLPNTHWLEGALERNRMGEIIIDAKCETSVKGVFAAGDCTTVPYKQIIIATGEGAKASLSAFDYLIRTKIA 521
               SCOP domains d1hyua3 A:1-102 Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain                     d1hyua4 A:103-198 Alkyl hydroperoxide reductase subunit F (AhpF), N-terminal domain             d1hyua1 A:199-325,A:452-521 Alkyl hydroperoxide reductase subunit F (AhpF), C-terminal domains                                 d1hyua2 A:326-451 Alkyl hydroperoxide reductase subunit F (AhpF), C-terminal domains                                          d1hyua1 A:199-325,A:452-521                                            SCOP domains
               CATH domains 1hyuA04 A:1-94 Glutaredoxin                                                                   --------1hyuA02 A:103-197 Glutaredoxin                                                                 --------------1hyuA01 A:212-324,A:453-521  [code=3.50.50.60, no name defined]                                                  --1hyuA03 A:327-449  [code=3.50.50.60, no name defined]                                                                      ---1hyuA01 A:212-324,A:453-521  [code=3.50.50.60, no name defined]       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhhhhhh....eeeee.........eeeee........eee...hhhhhhhhhhhhhhhh......hhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhh......eeee..eeeee...hhhhhhhhhh....hhhhhhhhh...eeeeee..hhhhhhhhhhhhhh...eeee....hhhhh..............hhhhhhhhhhhhhhh..eeee....eeeee........eeeee....eeeeeeeee...eee...............ee.....hhhhhh..eeeee..hhhhhhhhhhhhhhh.eeeee........hhhhhhhhh....eeee..eeeeeeee....eeeeeeee.....eeeee..eeee...eee.hhhhh.......................eee..........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------GLUTAREDOXIN_2  PDB: A:109-208 UniProt: 109-208                                                     ----------------------------------------------------------------------------------------------------------------------------------------PYRIDINE_REDOX_2     ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hyu A   1 MLDTNMKTQLRAYLEKLTKPVELIATLDDSAKSAEIKELLAEIAELSDKVTFKEDNTLPVRKPSFLITNPGSQQGPRFAGSPLGHEFTSLVLALLWTGGHPSKEAQSLLEQIRDIDGDFEFETYYSLSCHNCPDVVQALNLMAVLNPRIKHTAIDGGTFQNEITERNVMGVPAVFVNGKEFGQGRMTLTEIVAKVDTGAEKRAAEALNKRDAYDVLIVGSGPAGAAAAVYSARKGIRTGLMGERFGGQVLDTVDIENYISVPKTEGQKLAGALKAHVSDYDVDVIDSQSASKLVPAATEGGLHQIETASGAVLKARSIIIATGAKWRNMNVPGEDQYRTKGVTYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVEHVTLLEFAPEMKADQVLQDKVRSLKNVDIILNAQTTEVKGDGSKVVGLEYRDRVSGDIHSVALAGIFVQIGLLPNTHWLEGALERNRMGEIIIDAKCETSVKGVFAAGDCTTVPYKQIIIATGEGAKASLSAFDYLIRTKIA 521
                                    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       450       460       470       480       490       500       510       520
   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) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (AHPF_SALTY | P19480)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0008785    alkyl hydroperoxide reductase activity    Catalysis of the reaction: octane hydroperoxide + NADH + H+ = H2O + NAD+ + 1-octanol.
    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: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:0016651    oxidoreductase activity, acting on NAD(P)H    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    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:0000302    response to reactive oxygen species    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
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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  1hyu
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  AHPF_SALTY | P19480
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 Related Entries

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

UniProtKB/Swiss-Prot
        AHPF_SALTY | P19480: 1zyn 1zyp

(-) Related Entries Specified in the PDB File

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