3MBG - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN AUGMENTER OF LIVER REGENERATION (ALR)

Authors :   M. Dong, S. Schaefer, V. N. Daithankar, C. Thorpe, B. J. Bahnson

Date :   25 Mar 10 (Deposition) - 21 Jul 10 (Release) - 25 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Flavin, Flavoprotein, Sulfhydryl Oxidase, Fad, Gfer, Alr (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. N. Daithankar, S. A. Schaefer, M. Dong, B. J. Bahnson, C. Thorpe
Structure Of The Human Sulfhydryl Oxidase Augmenter Of Live Regeneration And Characterization Of A Human Mutation Causing An Autosomal Recessive Myopathy .
Biochemistry V. 49 6737 2010
PubMed-ID: 20593814 | Reference-DOI: 10.1021/BI100912M

Molecule 1 - FAD-LINKED SULFHYDRYL OXIDASE ALR
	Chains	:	A, B, C
	EC Number	:	1.8.3.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRCHIS A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SHORT FORM ALR (RESIDUES 81-205)
	Gene	:	GFER, ALR, HERV1, HPO
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	AUGMENTER OF LIVER REGENERATION, HERV1, HEPATOPOIETIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 28)

No.	Name	Count	Type	Full Name
1	ACT	11	Ligand/Ion	ACETATE ION
2	FAD	3	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NA	4	Ligand/Ion	SODIUM ION
4	ZN	10	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	ACT	10	Ligand/Ion	ACETATE ION
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NA	-1	Ligand/Ion	SODIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	ACT	6	Ligand/Ion	ACETATE ION
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NA	-1	Ligand/Ion	SODIUM ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (28, 28)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ZN A:3 , HOH A:22 , HOH A:27 , HOH A:47 , HOH A:59 , HOH A:64 , ARG A:99 , GLU A:100 , GLY A:103 , ARG A:104 , TRP A:107 , HIS A:111 , CYS A:145 , LEU A:149 , 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 , ACT A:207 , HOH A:211 , HOH A:232 , HOH A:439 , ASP B:159 , ARG B:161 , HOH B:229	BINDING SITE FOR RESIDUE FAD A 300
02	AC2	SOFTWARE	ASP A:159 , ACT A:206 , GLU C:100 , FAD C:300 , HOH C:441	BINDING SITE FOR RESIDUE ZN A 2
03	AC3	SOFTWARE	GLU A:100 , ACT A:207 , FAD A:300 , HOH A:439 , ASP B:159	BINDING SITE FOR RESIDUE ZN A 3
04	AC4	SOFTWARE	ASP A:98	BINDING SITE FOR RESIDUE NA A 9
05	AC5	SOFTWARE	GLU A:101 , HIS A:105 , ACT A:600 , ACT A:700	BINDING SITE FOR RESIDUE ZN A 1
06	AC6	SOFTWARE	ZN A:1 , HOH A:28 , GLU A:101 , ARG A:104 , HIS A:105 , ACT A:700	BINDING SITE FOR RESIDUE ACT A 600
07	AC7	SOFTWARE	ZN A:1 , GLU A:101 , HIS A:105 , ACT A:600	BINDING SITE FOR RESIDUE ACT A 700
08	AC8	SOFTWARE	ARG B:99 , GLU B:100 , GLY B:103 , ARG B:104 , TRP B:107 , HIS B:111 , CYS B:145 , LEU B:149 , CYS B:171 , HIS B:174 , ASN B:175 , VAL B:177 , ASN B:178 , LYS B:180 , LEU B:181 , LYS B:183 , PHE B:186 , ARG B:194 , TRP B:195 , HOH B:217 , HOH B:246 , HOH B:285 , HOH B:292 , HOH B:440 , ASP C:159 , ARG C:161 , HOH C:285 , HOH C:310 , ACT C:800	BINDING SITE FOR RESIDUE FAD B 300
09	AC9	SOFTWARE	ASP B:98	BINDING SITE FOR RESIDUE NA B 7
10	BC1	SOFTWARE	GLU B:101 , HIS B:105 , ACT B:700 , ACT C:600	BINDING SITE FOR RESIDUE ZN B 1
11	BC2	SOFTWARE	ZN B:1 , GLU B:101 , HIS B:105 , ACT B:700 , ARG C:104 , HIS C:105 , HOH C:313	BINDING SITE FOR RESIDUE ACT C 600
12	BC3	SOFTWARE	ZN B:1 , GLU B:101 , HIS B:105 , HOH B:283 , ACT C:600 , ACT C:700	BINDING SITE FOR RESIDUE ACT B 700
13	BC4	SOFTWARE	ZN A:2 , HOH A:7 , ASP A:159 , ARG A:161 , ACT A:206 , HOH B:307 , ARG C:99 , GLU C:100 , GLY C:103 , ARG C:104 , TRP C:107 , HIS C:111 , CYS C:145 , LEU C:149 , CYS C:171 , HIS C:174 , ASN C:175 , VAL C:177 , ASN C:178 , LYS C:180 , LEU C:181 , LYS C:183 , PHE C:186 , ARG C:194 , TRP C:195 , HOH C:280 , HOH C:291 , HOH C:323 , HOH C:325 , HOH C:359 , HOH C:441	BINDING SITE FOR RESIDUE FAD C 300
14	BC5	SOFTWARE	GLU B:100 , HOH B:440 , ASP C:159 , ACT C:800	BINDING SITE FOR RESIDUE ZN C 1
15	BC6	SOFTWARE	ASP C:98 , HOH C:432	BINDING SITE FOR RESIDUE NA C 8
16	BC7	SOFTWARE	ACT B:600 , GLU C:101 , HIS C:105 , ACT C:700	BINDING SITE FOR RESIDUE ZN C 2
17	BC8	SOFTWARE	ARG B:104 , HIS B:105 , HOH B:271 , ZN C:2 , GLU C:101 , HIS C:105 , ACT C:700	BINDING SITE FOR RESIDUE ACT B 600
18	BC9	SOFTWARE	ACT B:600 , ACT B:700 , ZN C:2 , GLU C:101 , HIS C:105 , HOH C:387	BINDING SITE FOR RESIDUE ACT C 700
19	CC1	SOFTWARE	ZN A:2 , ASP A:159 , ARG A:161 , THR A:162 , ALA A:165 , GLU C:100 , LYS C:183 , FAD C:300	BINDING SITE FOR RESIDUE ACT A 206
20	CC2	SOFTWARE	ZN A:3 , GLU A:100 , LYS A:183 , FAD A:300 , ASP B:159 , ARG B:161 , THR B:162 , ALA B:165	BINDING SITE FOR RESIDUE ACT A 207
21	CC3	SOFTWARE	GLU B:100 , LEU B:181 , LYS B:183 , FAD B:300 , ZN C:1 , ASP C:159 , ARG C:161 , ALA C:165	BINDING SITE FOR RESIDUE ACT C 800
22	CC4	SOFTWARE	HIS B:134 , HIS B:157 , HOH B:425 , HOH B:468 , HOH B:469	BINDING SITE FOR RESIDUE ZN B 206
23	CC5	SOFTWARE	GLU A:147 , HIS B:172 , GLU B:176 , ARG B:179	BINDING SITE FOR RESIDUE ZN B 2
24	CC6	SOFTWARE	HIS A:172 , GLU A:176 , ARG A:179 , GLU C:147	BINDING SITE FOR RESIDUE ZN A 208
25	CC7	SOFTWARE	GLU B:147 , HOH B:273 , HIS C:172 , GLU C:176 , ARG C:179	BINDING SITE FOR RESIDUE ZN C 4
26	CC8	SOFTWARE	LYS B:138 , HOH B:210 , GLU C:124 , ASP C:128	BINDING SITE FOR RESIDUE NA C 206
27	CC9	SOFTWARE	HIS C:134 , HIS C:157 , PRO C:158 , HOH C:470	BINDING SITE FOR RESIDUE ACT C 900
28	DC1	SOFTWARE	HIS A:134 , HIS A:157 , PRO A:158 , HOH A:471	BINDING SITE FOR RESIDUE ACT A 500

Asymmetric Unit

No.	Residues
1	A:95	-	A:204
2	A:142	-	A:145
3	A:171	-	A:188
4	B:95	-	C:204
5	B:142	-	B:145
6	B:171	-	B:188
7	B:204	-	C:95
8	C:142	-	C:145
9	C:171	-	C:188

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

Asymmetric Unit (2, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061994	F	166	L	ALR_HUMAN	Polymorphism	36041021	A/B/C	F	166	L
2	UniProt	VAR_063435	R	194	H	ALR_HUMAN	Disease (MPMCHD)	121908192	A/B/C	R	194	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061994	F	166	L	ALR_HUMAN	Polymorphism	36041021	A	F	166	L
2	UniProt	VAR_063435	R	194	H	ALR_HUMAN	Disease (MPMCHD)	121908192	A	R	194	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_061994	F	166	L	ALR_HUMAN	Polymorphism	36041021	B/C	F	166	L
2	UniProt	VAR_063435	R	194	H	ALR_HUMAN	Disease (MPMCHD)	121908192	B/C	R	194	H

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ERV_ALR	PS51324	ERV/ALR sulfhydryl oxidase domain profile.	ALR_HUMAN	95-195	3	A:95-195 B:95-195 C:95-195

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_HUMAN	95-195	2	A:95-195 - -

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_HUMAN	95-195	2	- B:95-195 C:95-195

(no "Exon" information available for 3MBG)

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:112
 aligned with ALR_HUMAN | P55789 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:112
                                   103       113       123       133       143       153       163       173       183       193       203  
            ALR_HUMAN    94 DCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLCRNHPDTRTRACFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 205
               SCOP domains d3mbga_ 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
                 3mbg A  94 DCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLARNHPDTRTRAAFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 205
                                   103       113       123       133       143       153       163       173       183       193       203

Chain B from PDB  Type:PROTEIN  Length:112
 aligned with ALR_HUMAN | P55789 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:112
                                   103       113       123       133       143       153       163       173       183       193       203  
            ALR_HUMAN    94 DCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLCRNHPDTRTRACFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 205
               SCOP domains d3mbgb_ B: 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: B:95-195 UniProt: 95-195                                                               ---------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3mbg B  94 DCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLARNHPDTRTRAAFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 205
                                   103       113       123       133       143       153       163       173       183       193       203

Chain C from PDB  Type:PROTEIN  Length:112
 aligned with ALR_HUMAN | P55789 from UniProtKB/Swiss-Prot  Length:205

    Alignment length:112
                                   103       113       123       133       143       153       163       173       183       193       203  
            ALR_HUMAN    94 DCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLCRNHPDTRTRACFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 205
               SCOP domains d3mbgc_ C: Augmenter of liver regeneration                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------Evr1_Alr-3mbgC01 C:104-197                                                                    -------- Pfam domains (1)
           Pfam domains (2) ----------Evr1_Alr-3mbgC02 C:104-197                                                                    -------- Pfam domains (2)
           Pfam domains (3) ----------Evr1_Alr-3mbgC03 C:104-197                                                                    -------- Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------L---------------------------H----------- SAPs(SNPs)
                    PROSITE -ERV_ALR  PDB: C:95-195 UniProt: 95-195                                                               ---------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 3mbg C  94 DCPPDREELGRHSWAVLHTLAAYYPDLPTPEQQQDMAQFIHLFSKFYPCEECAEDLRKRLARNHPDTRTRAAFTQWLCHLHNEVNRKLGKPDFDCSKVDERWRDGWKDGSCD 205
                                   103       113       123       133       143       153       163       173       183       193       203

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	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)

Human (Homo sapiens) [TaxId: 9606] (6)

1a	d3mbga_	A:
1b	d3mbgb_	B:
1c	d3mbgc_	C:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: Evr1_Alr (7)

Homo sapiens (Human) (4)

1a	Evr1_Alr-3mbgC01	C:104-197
1b	Evr1_Alr-3mbgC02	C:104-197
1c	Evr1_Alr-3mbgC03	C:104-197

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mbg)

Biological Units
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Access by PDB/NDB ID
	3mbg
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	ALR_HUMAN \| P55789
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	1.8.3.2
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	613076
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	ALR_HUMAN \| P55789
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UniProtKB/Swiss-Prot
	ALR_HUMAN \| P55789	:	3o55 3tk0 3u2l 3u2m 3u5s 4ldk

(no "Related Entries Specified in the PDB File" available for 3MBG)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 28)

Sites (28, 28)

SS Bonds (9, 9)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 6)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (1, 3)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File