1HY0 - JenaLib

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Title :   CRYSTAL STRUCTURE OF WILD TYPE DUCK DELTA 1 CRYSTALLIN (EYE LENS PROTEIN)

Authors :   L. M. Sampaleanu, F. Vallee, C. Slingsby, P. L. Howell

Date :   17 Jan 01 (Deposition) - 21 Apr 01 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Eye Lens Protein, Delta 1 Crystallin, Argininosuccinate Lyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. M. Sampaleanu, F. Vallee, C. Slingsby, P. L. Howell
Structural Studies Of Duck Delta 1 And Delta 2 Crystallin Suggest Conformational Changes Occur During Catalysis.
Biochemistry V. 40 2732 2001
PubMed-ID: 11258884 | Reference-DOI: 10.1021/BI002272K

Molecule 1 - DELTA CRYSTALLIN I
	Chains	:	A, B
	EC Number	:	4.3.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET17B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ANAS PLATYRHYNCHOS
	Organism Taxid	:	8839
	Synonym	:	DELTA-1-CRYSTALLIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:281 , MET A:284 , LYS A:287 , ASN A:289 , ASN B:114 , THR B:159 , HIS B:160 , HOH B:1109 , HOH B:1231	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	ASN A:114 , THR A:159 , HIS A:160 , SER B:281 , MET B:284 , LYS B:287 , ASN B:289 , HOH B:1034	BINDING SITE FOR RESIDUE SO4 B 1002

(no "SS Bond" information available for 1HY0)

Asymmetric Unit

No.	Residues
1	Ser A:319	-	Thr A:320
2	Ser B:319	-	Thr B:320

(no "SAP(SNP)/Variant" information available for 1HY0)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FUMARATE_LYASES	PS00163	Fumarate lyases signature.	ARLY1_ANAPL	280-289	2	A:280-289 B:280-289

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FUMARATE_LYASES	PS00163	Fumarate lyases signature.	ARLY1_ANAPL	280-289	4	A:280-289 B:280-289

(no "Exon" information available for 1HY0)

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:447
 aligned with ARLY1_ANAPL | P24057 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:447
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       
          ARLY1_ANAPL    18 DPIMQMLSTSISTEQRLSEVDIQASIAYAKALEKAGILTKTELEKILSGLEKISEELSKGVIVVTQSDEDIQTANERRLKELIGDIAGKLHTGRSRNEQVVTDLKLFMKNSLSIISTHLLQLIKTLVERAAIEIDVILPGYTHLQKAQPIRWSQFLLSHAVALTRDSERLGEVKKRINVLPLGSGALAGNPLDIDREMLRSELEFASISLNSMDAISERDFVVEFLSVATLLLIHLSKMAEDLIIYSTSEFGFLTLSDAFSTGSSLMPQKKNPDSLELIRSKAGRVFGRLASILMVLKGLPSTYNKDLQEDKEAVIDVVDTLTAVLQVATGVISTLQISKENMEKALTPEMLATDLALYLVRKGMPFRQAHTASGKAVHLAETKGIAINNLTLEDLKSISPLFSSDVSQVFNFVNSVEQYTALGGTAKSSVTTQIEQLRELMKKQKE 464
               SCOP domains d1hy0a_ A: Argininosuccinate lyase/delta-crystallin                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------1hy0A01 A:27-123,A:195-234 Fumarase/aspartase (N-terminal domain)                                1hy0A02 A:124-194,A:235-364,A:437-463                                  1hy0A01 A:27-123,A:195-234              1hy0A02 A:124-194,A:235-364,A:437-463 Fumarase/aspartase (Central domain)                                                         1hy0A03 A:365-436 Fumarase/aspartase (C-terminal domain)                1hy0A02                    - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhee..............hhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh......hhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hy0 A  18 DPIMQMLSTSISTEQRLSEVDIQASIAYAKALEKAGILTKTELEKILSGLEKISEELSKGVIVVTQSDEDIQTANERRLKELIGDIAGKLHTGRSRNEQVVTDLKLFMKNSLSIISTHLLQLIKTLVERAAIEIDVILPGYTHLQKAQPIRWSQFLLSHAVALTRDSERLGEVKKRINVLPLGSGALAGNPLDIDREMLRSELEFASISLNSMDAISERDFVVEFLSVATLLLIHLSKMAEDLIIYSTSEFGFLTLSDAFSTGSSLMPQKKNPDSLELIRSKSGRVFGRLASILMVLKGLPSTYNKDLQEDKEAVIDVVDTLTAVLQVATGVISTLQISKENMEKALTPEMLATDLALYLVRKGMPFRQAHTASGKAVHLAETKGIAINNLTLEDLKSISPLFSSDVSQVFNFVNSVEQYTALGGTAKSSVTTQIEQLRELMKKQKE 464
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457

Chain B from PDB  Type:PROTEIN  Length:448
 aligned with ARLY1_ANAPL | P24057 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:448
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457        
          ARLY1_ANAPL    18 DPIMQMLSTSISTEQRLSEVDIQASIAYAKALEKAGILTKTELEKILSGLEKISEELSKGVIVVTQSDEDIQTANERRLKELIGDIAGKLHTGRSRNEQVVTDLKLFMKNSLSIISTHLLQLIKTLVERAAIEIDVILPGYTHLQKAQPIRWSQFLLSHAVALTRDSERLGEVKKRINVLPLGSGALAGNPLDIDREMLRSELEFASISLNSMDAISERDFVVEFLSVATLLLIHLSKMAEDLIIYSTSEFGFLTLSDAFSTGSSLMPQKKNPDSLELIRSKAGRVFGRLASILMVLKGLPSTYNKDLQEDKEAVIDVVDTLTAVLQVATGVISTLQISKENMEKALTPEMLATDLALYLVRKGMPFRQAHTASGKAVHLAETKGIAINNLTLEDLKSISPLFSSDVSQVFNFVNSVEQYTALGGTAKSSVTTQIEQLRELMKKQKEQ 465
               SCOP domains d1hy0b_ B: Argininosuccinate lyase/delta-crystallin                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ---------1hy0B01 B:27-123,B:195-234 Fumarase/aspartase (N-terminal domain)                                1hy0B02 B:124-194,B:235-364,B:437-463                                  1hy0B01 B:27-123,B:195-234              1hy0B02 B:124-194,B:235-364,B:437-463 Fumarase/aspartase (Central domain)                                                         1hy0B03 B:365-436 Fumarase/aspartase (C-terminal domain)                1hy0B02                    -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhee..............hhhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......ee.hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FUMARATE_L-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hy0 B  18 DPIMQMLSTSISTEQRLSEVDIQASIAYAKALEKAGILTKTELEKILSGLEKISEELSKGVIVVTQSDEDIQTANERRLKELIGDIAGKLHTGRSRNEQVVTDLKLFMKNSLSIISTHLLQLIKTLVERAAIEIDVILPGYTHLQKAQPIRWSQFLLSHAVALTRDSERLGEVKKRINVLPLGSGALAGNPLDIDREMLRSELEFASISLNSMDAISERDFVVEFLSVATLLLIHLSKMAEDLIIYSTSEFGFLTLSDAFSTGSSLMPQKKNPDSLELIRSKSGRVFGRLASILMVLKGLPSTYNKDLQEDKEAVIDVVDTLTAVLQVATGVISTLQISKENMEKALTPEMLATDLALYLVRKGMPFRQAHTASGKAVHLAETKGIAINNLTLEDLKSISPLFSSDVSQVFNFVNSVEQYTALGGTAKSSVTTQIEQLRELMKKQKEQ 465
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457

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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: L-aspartase-like (67)

Superfamily: L-aspartase-like (67)

Family: L-aspartase/fumarase (39)

Protein domain: Argininosuccinate lyase/delta-crystallin (14)

Domestic duck (Anas platyrhynchos), delta-crystallin [TaxId: 8839] (10)

1a	d1hy0a_	A:
1b	d1hy0b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Fumarase C; Chain B, domain 1 (57)

Homologous Superfamily: Fumarase/aspartase (N-terminal domain) (57)

Anas platyrhynchos. Organism_taxid: 8839. (8)

1a	1hy0A01	A:27-123,A:195-234
1b	1hy0B01	B:27-123,B:195-234

Topology: Ribonucleotide Reductase Protein R1; domain 1 (62)

Homologous Superfamily: Fumarase/aspartase (C-terminal domain) (42)

Anas platyrhynchos. Organism_taxid: 8839. (8)

2a	1hy0A03	A:365-436
2b	1hy0B03	B:365-436

Architecture: Up-down Bundle (3216)

Topology: Fumarase C; Chain A, domain 2 (60)

Homologous Superfamily: Fumarase/aspartase (Central domain) (59)

Anas platyrhynchos. Organism_taxid: 8839. (8)

3a	1hy0A02	A:124-194,A:235-364,A:437-463
3b	1hy0B02	B:124-194,B:235-364,B:437-463

(no "Pfam Domain" information available for 1HY0)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ARLY1_ANAPL | P24057)

molecular function
	GO:0004056	argininosuccinate lyase activity	Catalysis of the reaction: N-(L-arginino)succinate = fumarate + L-arginine.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0005212	structural constituent of eye lens	The action of a molecule that contributes to the structural integrity of the lens of an eye.
biological process
	GO:0042450	arginine biosynthetic process via ornithine	The chemical reactions and pathways resulting in the formation of arginine (2-amino-5-guanidinopentanoic acid) via the intermediate compound ornithine.

Asymmetric Unit
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	Cis Peptide Bonds
		Ser A:319 - Thr A:320	[ RasMol ]
		Ser B:319 - Thr B:320	[ RasMol ]

Biological Unit
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		Biological Unit 1	[ Jena3D ]

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	1hy0
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	ARLY1_ANAPL \| P24057	:	1u15 1u16

1aos	ARGININOSUCCINATE LYASE (HUMAN)
1auw	DUCK DELTA 2 CRYSTALLIN H89N MUTANT
1dcn	DUCK DELTA 2 CRYSTALLIN H162N MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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