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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN FAD-LINKED AUGMENTER OF LIVER REGENERATION (ALR)
 
Authors :  L. Banci, I. Bertini, V. Calderone, C. Cefaro, S. Ciofi-Baffoni, A. Gal E. Kallergi, E. Lionaki, C. Pozidis, K. Tokatlidis
Date :  28 Jul 10  (Deposition) - 13 Apr 11  (Release) - 13 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Flavin, Flavoprotein, Sulfhydryl Oxidase, Fad, Gfer, Alr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Banci, I. Bertini, V. Calderone, C. Cefaro, S. Ciofi-Baffoni, A. Gallo, E. Kallergi, E. Lionaki, C. Pozidis, K. Tokatlidis
Molecular Recognition And Substrate Mimicry Drive The Electron-Transfer Process Between Mia40 And Alr.
Proc. Natl. Acad. Sci. Usa V. 108 4811 2011
PubMed-ID: 21383138  |  Reference-DOI: 10.1073/PNAS.1014542108

(-) Compounds

Molecule 1 - AUGMENTER OF LIVER REGENERATION
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 80 TO 204
    Gene: ALR
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:23 , GLU A:24 , GLY A:27 , ARG A:28 , SER A:30 , TRP A:31 , HIS A:35 , TYR A:64 , CYS A:69 , LEU A:73 , CYS A:95 , HIS A:98 , ASN A:99 , VAL A:101 , ASN A:102 , LYS A:104 , LEU A:105 , LYS A:107 , PHE A:110 , ARG A:118 , TRP A:119 , HOH A:136 , HOH A:157 , HOH A:180 , HOH A:183 , HOH A:200 , HOH A:202 , HOH A:222 , HOH A:223 , HOH A:269BINDING SITE FOR RESIDUE FAD A 0

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:19 -A:128
2A:66 -A:69
3A:95 -A:112

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O55)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061994F166LALR_HUMANPolymorphism36041021AF90L
2UniProtVAR_063435R194HALR_HUMANDisease (MPMCHD)121908192AR118H
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061994F166LALR_HUMANPolymorphism36041021AF90L
2UniProtVAR_063435R194HALR_HUMANDisease (MPMCHD)121908192AR118H
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ERV_ALRPS51324 ERV/ALR sulfhydryl oxidase domain profile.ALR_HUMAN95-195  1A:19-119
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ERV_ALRPS51324 ERV/ALR sulfhydryl oxidase domain profile.ALR_HUMAN95-195  2A:19-119

(-) Exons   (0, 0)

(no "Exon" information available for 3O55)

(-) 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:115
 aligned with ALR_HUMAN | P55789 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:115
                                   100       110       120       130       140       150       160       170       180       190       200     
            ALR_HUMAN    91 FREDCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLCRNHPDTRTRACFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 205
               SCOP domains d3o55a_ A: Augmenter of liver regeneration                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Evr1_Alr-3o55A01 A:28-121                                                                     -------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------L---------------------------H----------- SAPs(SNPs)
                    PROSITE ----ERV_ALR  PDB: A:19-119 UniProt: 95-195                                                               ---------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3o55 A  15 FREDCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLARNHPDTRTRAAFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 129
                                    24        34        44        54        64        74        84        94       104       114       124     


Chain A from PDB  Type:PROTEIN  Length:115
 aligned with Q9NY86_HUMAN | Q9NY86 from UniProtKB/TrEMBL  Length:204

    Alignment length:115
                                    99       109       119       129       139       149       159       169       179       189       199     
         Q9NY86_HUMAN    90 FREDCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLCRNHPDTRTRACFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 204
               SCOP domains d3o55a_ A: Augmenter of liver regeneration                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------Evr1_Alr-3o55A01 A:28-121                                                                     -------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------L---------------------------H----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3o55 A  15 FREDCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLARNHPDTRTRAAFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 129
                                    24        34        44        54        64        74        84        94       104       114       124
   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  (1, 1)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O55)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Evr1_Alr] (7)

(-) Gene Ontology  (11, 14)

Asymmetric Unit(hide GO term definitions)
Chain A   (ALR_HUMAN | P55789)
molecular function
    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:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0015035    protein disulfide oxidoreductase activity    Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
    GO:0016972    thiol oxidase activity    Catalysis of the reaction: 4 R'C(R)SH + O2 = 2 R'C(R)S-S(R)CR' + 2 H2O.
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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Chain A   (Q9NY86_HUMAN | Q9NY86)
molecular function
    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:0016972    thiol oxidase activity    Catalysis of the reaction: 4 R'C(R)SH + O2 = 2 R'C(R)S-S(R)CR' + 2 H2O.
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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  3o55
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  ALR_HUMAN | P55789
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  Q9NY86_HUMAN | Q9NY86
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 Related Entries

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

UniProtKB/Swiss-Prot
        ALR_HUMAN | P55789: 3mbg 3tk0 3u2l 3u2m 3u5s 4ldk

(-) Related Entries Specified in the PDB File

2hj3 GAIN OF FUNCTION IN AN ERV/ALR SULFHYDRYL OXIDASE BY MOLECULAR ENGINEERING OF THE SHUTTLE DISULFIDE.
3mbg STRUCTURE OF THE HUMAN SULFHYDRYL OXIDASE AUGMENTER OF LIVER REGENERATION AND CHARACTERIZATION OF A HUMAN MUTATION CAUSING AN AUTOSOMAL RECESSIVE MYOPATHY.