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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ALR MUTANT C142S.
 
Authors :  L. Banci, I. Bertini, V. Calderone, C. Cefaro, S. Ciofi-Baffoni, A. Gal
Date :  04 Oct 11  (Deposition) - 06 Jun 12  (Release) - 06 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Flavoprotein, Alr, Sulfhydryl Oxidase, Flavin, Fad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Banci, I. Bertini, V. Calderone, C. Cefaro, S. Ciofi-Baffoni, A. Gallo, K. Tokatlidis
An Electron-Transfer Path Through An Extended Disulfide Relay System: The Case Of The Redox Protein Alr.
J. Am. Chem. Soc. V. 134 1442 2012
PubMed-ID: 22224850  |  Reference-DOI: 10.1021/JA209881F
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAD-LINKED SULFHYDRYL OXIDASE ALR
    Chains: A
    EC Number: 1.8.3.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PDEST-HIS-MBP
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 91-205
    Gene: GFER, ALR, HERV1, HPO
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AUGMENTER OF LIVER REGENERATION, HERV1, HEPATOPOIETIN

 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
1AC1SOFTWAREGLY A:103 , ARG A:104 , SER A:106 , TRP A:107 , HIS A:111 , TYR A:140 , CYS A:145 , CYS A:171 , HIS A:174 , ASN A:175 , VAL A:177 , ASN A:178 , LYS A:180 , LEU A:181 , LYS A:183 , PHE A:186 , ARG A:194 , TRP A:195 , HOH A:417 , HOH A:424 , HOH A:426 , HOH A:444 , HOH A:474 , HOH A:500BINDING SITE FOR RESIDUE FAD A 301

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:95 -A:204
2A:171 -A:188

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3U2L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061994F166LALR_HUMANPolymorphism36041021AF166L
2UniProtVAR_063435R194HALR_HUMANDisease (MPMCHD)121908192AR194H
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_061994F166LALR_HUMANPolymorphism36041021AF166L
2UniProtVAR_063435R194HALR_HUMANDisease (MPMCHD)121908192AR194H
  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:95-195
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ERV_ALRPS51324 ERV/ALR sulfhydryl oxidase domain profile.ALR_HUMAN95-195  2A:95-195

(-) Exons   (0, 0)

(no "Exon" information available for 3U2L)

(-) 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 d3u2la_ A: Augmenter of liver regeneration                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------L---------------------------H----------- SAPs(SNPs)
                    PROSITE ----ERV_ALR  PDB: A:95-195 UniProt: 95-195                                                               ---------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 3u2l A  91 FREDCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPSEECAEDLRKRLARNHPDTRTRAAFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 205
                                   100       110       120       130       140       150       160       170       180       190       200
   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 3U2L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3U2L)

(-) Gene Ontology  (11, 11)

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ALR_HUMAN | P55789: 3mbg 3o55 3tk0 3u2m 3u5s 4ldk

(-) Related Entries Specified in the PDB File

3o55 CRYSTAL STRUCTURE OF HUMAN FAD-LINKED AUGMENTER OF LIVER REGENERATION (ALR)
3u2m