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Title :   THE CRYSTAL STRUCTURE OF AUGMENTER OF LIVER REGENERATION: A MAMMALIAN FAD DEPENDENT SULFHYDRYL OXIDASE

Authors :   J. P. Rose, C. -K. Wu, B. -C. Wang

Date :   07 Mar 03 (Deposition) - 15 Apr 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,C  (1x)
Biol. Unit 2: B,D  (1x)

Keywords :   Sulfhydryl Oxidase, Liver Regeneration, Alr, Helix-Turn-Helix, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. -K. Wu, T. A. Dailey, H. A. Dailey, B. -C. Wang, J. P. Rose
The Refined Crystal Structure Of Augmenter Of Liver Regeneration
Int. Union Cryst. (Meeting) V. 1 293 1999
PubMed: search | Reference-DOI: 10.1109/ACC.1999.782787
(for further references see the PDB file header)

Molecule 1 - AUGMENTER OF LIVER REGENERATION
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET16
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	ALR
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	ALR

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:19 , GLU A:20 , GLY A:23 , ARG A:24 , TRP A:27 , HIS A:31 , PHE A:56 , TYR A:60 , CYS A:65 , ILE A:69 , CYS A:91 , HIS A:94 , ASN A:95 , VAL A:97 , ASN A:98 , LYS A:100 , LEU A:101 , LYS A:103 , PHE A:106 , ARG A:114 , TRP A:115 , HOH A:131 , HOH A:148 , HOH A:150 , HOH A:165 , HOH A:195 , HOH A:201 , HOH A:203 , HOH A:252 , HOH A:266	BINDING SITE FOR RESIDUE FAD A 126
2	AC2	SOFTWARE	ARG B:19 , GLU B:20 , GLY B:23 , ARG B:24 , TRP B:27 , HIS B:31 , PHE B:56 , TYR B:60 , CYS B:65 , CYS B:91 , HIS B:94 , ASN B:95 , VAL B:97 , ASN B:98 , LYS B:100 , LEU B:101 , LYS B:103 , PHE B:106 , ARG B:114 , TRP B:115 , HOH B:135 , HOH B:152 , HOH B:167 , HOH B:174 , HOH B:192 , HOH B:198 , HOH B:215 , HOH B:232 , HOH B:276	BINDING SITE FOR RESIDUE FAD B 126
3	AC3	SOFTWARE	ARG C:19 , GLU C:20 , GLY C:23 , ARG C:24 , TRP C:27 , HIS C:31 , PHE C:56 , TYR C:60 , CYS C:65 , ILE C:69 , CYS C:91 , HIS C:94 , ASN C:95 , VAL C:97 , ASN C:98 , LYS C:100 , LEU C:101 , LYS C:103 , PHE C:106 , ARG C:114 , TRP C:115 , HOH C:139 , HOH C:162 , HOH C:179 , HOH C:185 , HOH C:189 , HOH C:233 , HOH C:263 , HOH C:274	BINDING SITE FOR RESIDUE FAD C 126
4	AC4	SOFTWARE	ARG D:19 , GLU D:20 , GLY D:23 , ARG D:24 , TRP D:27 , HIS D:31 , PHE D:56 , TYR D:60 , CYS D:65 , ASP D:68 , ILE D:69 , CYS D:91 , HIS D:94 , ASN D:95 , VAL D:97 , ASN D:98 , LYS D:100 , LEU D:101 , LYS D:103 , PHE D:106 , ARG D:114 , TRP D:115 , HOH D:144 , HOH D:148 , HOH D:159 , HOH D:162 , HOH D:164 , HOH D:183 , HOH D:187 , HOH D:193 , HOH D:261 , HOH D:269	BINDING SITE FOR RESIDUE FAD D 126
5	CTA	AUTHOR	CYS A:62 , CYS A:65 , FAD A:126	PUTATIVE CATALYTIC SITE
6	CTB	AUTHOR	CYS B:62 , CYS B:65 , FAD B:126	PUTATIVE CATALYTIC SITE
7	CTC	AUTHOR	CYS C:62 , CYS C:65 , FAD C:126	PUTATIVE CATALYTIC SITE
8	CTD	AUTHOR	CYS D:62 , CYS D:65 , FAD D:126	PUTATIVE CATALYTIC SITE

Asymmetric Unit

No.	Residues
1	A:15	-	C:124
2	A:62	-	A:65
3	A:91	-	A:108
4	A:124	-	C:15
5	B:15	-	D:124
6	B:62	-	B:65
7	B:91	-	B:108
8	B:124	-	D:15
9	C:62	-	C:65
10	C:91	-	C:108
11	D:62	-	D:65
12	D:91	-	D:108

(no "Cis Peptide Bond" information available for 1OQC)

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ERV_ALR	PS51324	ERV/ALR sulfhydryl oxidase domain profile.	ALR_RAT	88-188	4	A:15-115 B:15-115 C:15-115 D:15-115

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ERV_ALR	PS51324	ERV/ALR sulfhydryl oxidase domain profile.	ALR_RAT	88-188	2	A:15-115 - C:15-115 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ERV_ALR	PS51324	ERV/ALR sulfhydryl oxidase domain profile.	ALR_RAT	88-188	2	- B:15-115 - D:15-115

Asymmetric Unit (2, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSRNOT00000017917	1	ENSRNOE00000127312	chr10:13948665-13948348	318	ALR_RAT	1-79	79	0	-	-
1.2	ENSRNOT00000017917	2	ENSRNOE00000127401	chr10:13947976-13947780	197	ALR_RAT	80-145	66	4	A:13-72 B:14-72 C:13-72 D:13-72	60 59 60 60
1.3	ENSRNOT00000017917	3	ENSRNOE00000127645	chr10:13947020-13946311	710	ALR_RAT	145-198	54	4	A:72-124 B:72-124 C:72-124 D:72-124	53 53 53 53

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:112
 aligned with ALR_RAT | Q63042 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:112
                                    95       105       115       125       135       145       155       165       175       185       195  
              ALR_RAT    86 EDCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSC 197
               SCOP domains d1oqca_ A: Augmenter of liver regeneration                                                                       SCOP domains
               CATH domains 1oqcA00 A:13-124  [code=1.20.120.310, no name defined]                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ERV_ALR  PDB: A:15-115 UniProt: 88-188                                                               --------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:13-72 UniProt: 80-145 [INCOMPLETE]         ---------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.3  PDB: A:72-124 UniProt: 145-198 [INCOMPLETE] Transcript 1 (2)
                 1oqc A  13 EDCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSC 124
                                    22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:111
 aligned with ALR_RAT | Q63042 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:111
                                    96       106       116       126       136       146       156       166       176       186       196 
              ALR_RAT    87 DCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSC 197
               SCOP domains d1oqcb_ B: Augmenter of liver regeneration                                                                      SCOP domains
               CATH domains 1oqcB00 B:14-124  [code=1.20.120.310, no name defined]                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -ERV_ALR  PDB: B:15-115 UniProt: 88-188                                                               --------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:14-72 UniProt: 80-145 [INCOMPLETE]        ---------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.3  PDB: B:72-124 UniProt: 145-198 [INCOMPLETE] Transcript 1 (2)
                 1oqc B  14 DCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSC 124
                                    23        33        43        53        63        73        83        93       103       113       123

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with ALR_RAT | Q63042 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:112
                                    95       105       115       125       135       145       155       165       175       185       195  
              ALR_RAT    86 EDCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSC 197
               SCOP domains d1oqcc_ C: Augmenter of liver regeneration                                                                       SCOP domains
               CATH domains 1oqcC00 C:13-124  [code=1.20.120.310, no name defined]                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ERV_ALR  PDB: C:15-115 UniProt: 88-188                                                               --------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: C:13-72 UniProt: 80-145 [INCOMPLETE]         ---------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.3  PDB: C:72-124 UniProt: 145-198 [INCOMPLETE] Transcript 1 (2)
                 1oqc C  13 EDCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSC 124
                                    22        32        42        52        62        72        82        92       102       112       122

Chain D from PDB  Type:PROTEIN  Length:112
 aligned with ALR_RAT | Q63042 from UniProtKB/Swiss-Prot  Length:198

    Alignment length:112
                                    95       105       115       125       135       145       155       165       175       185       195  
              ALR_RAT    86 EDCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSC 197
               SCOP domains d1oqcd_ D: Augmenter of liver regeneration                                                                       SCOP domains
               CATH domains 1oqcD00 D:13-124  [code=1.20.120.310, no name defined]                                                           CATH domains
           Pfam domains (1) -----------Evr1_Alr-1oqcD01 D:24-117                                                                     ------- Pfam domains (1)
           Pfam domains (2) -----------Evr1_Alr-1oqcD02 D:24-117                                                                     ------- Pfam domains (2)
           Pfam domains (3) -----------Evr1_Alr-1oqcD03 D:24-117                                                                     ------- Pfam domains (3)
           Pfam domains (4) -----------Evr1_Alr-1oqcD04 D:24-117                                                                     ------- Pfam domains (4)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --ERV_ALR  PDB: D:15-115 UniProt: 88-188                                                               --------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: D:13-72 UniProt: 80-145 [INCOMPLETE]         ---------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.3  PDB: D:72-124 UniProt: 145-198 [INCOMPLETE] Transcript 1 (2)
                 1oqc D  13 EDCPQDREELGRNTWAFLHTLAAYYPDMPTPEQQQDMAQFIHIFSKFYPCEECAEDIRKRIDRSQPDTSTRVSFSQWLCRLHNEVNRKLGKPDFDCSRVDERWRDGWKDGSC 124
                                    22        32        42        52        62        72        82        92       102       112       122

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Four-helical up-and-down bundle (308)

Superfamily: FAD-dependent thiol oxidase (15)

Family: FAD-dependent thiol oxidase (10)

Protein domain: Augmenter of liver regeneration (7)

Norway rat (Rattus norvegicus) [TaxId: 10116] (1)

1a	d1oqca_	A:
1b	d1oqcb_	B:
1c	d1oqcc_	C:
1d	d1oqcd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.310, no name defined] (4)

Norway rat (Rattus norvegicus) (1)

1a	1oqcB00	B:14-124
1b	1oqcA00	A:13-124
1c	1oqcC00	C:13-124
1d	1oqcD00	D:13-124

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Evr1_Alr (7)

Rattus norvegicus (Rat) (1)

1a	Evr1_Alr-1oqcD01	D:24-117
1b	Evr1_Alr-1oqcD02	D:24-117
1c	Evr1_Alr-1oqcD03	D:24-117
1d	Evr1_Alr-1oqcD04	D:24-117

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ALR_RAT | Q63042)

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:0016971	flavin-linked sulfhydryl oxidase activity	Catalysis of the formation of disulfide bridges.
	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: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:0072717	cellular response to actinomycin D	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an actinomycin D stimulus.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0097237	cellular response to toxic substance	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
	GO:0071356	cellular response to tumor necrosis factor	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a tumor necrosis factor stimulus.
	GO:0097421	liver regeneration	The regrowth of lost or destroyed liver.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0045953	negative regulation of natural killer cell mediated cytotoxicity	Any process that stops, prevents, or reduces the rate of natural killer mediated cytotoxicity.
	GO:1903204	negative regulation of oxidative stress-induced neuron death	Any process that stops, prevents or reduces the frequency, rate or extent of oxidative stress-induced neuron death.
	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:2000573	positive regulation of DNA biosynthetic process	Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
	GO:0032496	response to lipopolysaccharide	Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	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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Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (8, 8)

SS Bonds (12, 12)

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