3A15 - JenaLib

Title :   CRYSTAL STRUCTURE OF SUBSTRATE-FREE FORM OF ALDOXIME DEHYDRATASE (OXDRE)

Authors :   H. Sawai, H. Sugimoto, Y. Kato, Y. Asano, Y. Shiro, S. Aono

Date :   26 Mar 09 (Deposition) - 08 Sep 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.79

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

Keywords :   Beta Barrel, Heme Protein, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Sawai, H. Sugimoto, Y. Kato, Y. Asano, Y. Shiro, S. Aono
X-Ray Crystal Structure Of Michaelis Complex Of Aldoxime Dehydratase
J. Biol. Chem. V. 284 32089 2009
PubMed-ID: 19740758 | Reference-DOI: 10.1074/JBC.M109.018762

Compounds

Molecule 1 - ALDOXIME DEHYDRATASE
	Chains	:	A, B, C, D
	EC Number	:	4.99.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	OXD
	Organism Scientific	:	RHODOCOCCUS ERYTHROPOLIS
	Organism Taxid	:	1833
	Synonym	:	OXDRE

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 4)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	HEM	4	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:27 , HIS A:169 , GLY A:170 , TYR A:171 , TRP A:172 , GLY A:173 , SER A:174 , MET A:175 , ILE A:217 , SER A:219 , ILE A:238 , MET A:246 , ASN A:279 , LEU A:289 , TRP A:292 , SER A:293 , HIS A:299 , ILE A:302 , PHE A:303 , PHE A:306 , PHE A:307 , HOH A:401 , HOH A:414 , HOH A:438 , HOH A:470 , HOH A:668	BINDING SITE FOR RESIDUE HEM A 354
2	AC2	SOFTWARE	PHE B:27 , LEU B:145 , HIS B:169 , GLY B:170 , TYR B:171 , TRP B:172 , GLY B:173 , SER B:174 , MET B:175 , ILE B:217 , SER B:219 , GLN B:221 , ILE B:238 , MET B:246 , ASN B:279 , LEU B:289 , TRP B:292 , SER B:293 , HIS B:299 , ILE B:302 , PHE B:303 , PHE B:306 , LEU B:318 , HOH B:401 , HOH B:413 , HOH B:418 , HOH B:625	BINDING SITE FOR RESIDUE HEM B 354
3	AC3	SOFTWARE	PHE C:27 , HIS C:169 , GLY C:170 , TYR C:171 , TRP C:172 , GLY C:173 , SER C:174 , MET C:175 , SER C:219 , ILE C:238 , MET C:246 , ASN C:279 , LEU C:289 , TRP C:292 , SER C:293 , HIS C:299 , ILE C:302 , PHE C:306 , PHE C:307 , HOH C:401 , HOH C:520 , HOH C:662 , HOH C:668 , HOH C:678	BINDING SITE FOR RESIDUE HEM C 354
4	AC4	SOFTWARE	PHE D:27 , LEU D:145 , HIS D:169 , GLY D:170 , TYR D:171 , TRP D:172 , GLY D:173 , SER D:174 , MET D:175 , SER D:219 , GLN D:221 , MET D:246 , ASN D:279 , LEU D:289 , TRP D:292 , SER D:293 , HIS D:299 , ILE D:302 , PHE D:303 , PHE D:306 , HOH D:401 , HOH D:539 , HOH D:722 , HOH D:790	BINDING SITE FOR RESIDUE HEM D 354

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:353
 aligned with Q76K71_RHOER | Q76K71 from UniProtKB/TrEMBL  Length:353

    Alignment length:353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   
         Q76K71_RHOER     1 MESAIGEHLQCPRTLTRRVPDTYTPPFPMWVGRADDALQQVVMGYLGVQFRDEDQRPAALQAMRDIVAGFDLPDGPAHHDLTHHIDNQGYENLIVVGYWKDVSSQHRWSTSTPIASWWESEDRLSDGLGFFREIVAPRAEQFETLYAFQEDLPGVGAVMDGISGEINEHGYWGSMRERFPISQTDWMQASGELRVIAGDPAVGGRVVVRGHDNIALIRSGQDWADAEADERSLYLDEILPTLQSGMDFLRDNGPAVGCYSNRFVRNIDIDGNFLDLSYNIGHWASLDQLERWSESHPTHLRIFTTFFRVAAGLSKLRLYHEVSVFDAADQLYEYINCHPGTGMLRDAVTIAEH 353
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.....................ee........eeeeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhh.eeeee......hhhhhhh.ee..........hhhhhhhhhhhh.........eeeeee...eeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee.....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeehhh.eeeeee.....hhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a15 A   1 MESAIGEHLQCPRTLTRRVPDTYTPPFPMWVGRADDALQQVVMGYLGVQFRDEDQRPAALQAMRDIVAGFDLPDGPAHHDLTHHIDNQGYENLIVVGYWKDVSSQHRWSTSTPIASWWESEDRLSDGLGFFREIVAPRAEQFETLYAFQEDLPGVGAVMDGISGEINEHGYWGSMRERFPISQTDWMQASGELRVIAGDPAVGGRVVVRGHDNIALIRSGQDWADAEADERSLYLDEILPTLQSGMDFLRDNGPAVGCYSNRFVRNIDIDGNFLDLSYNIGHWASLDQLERWSESHPTHLRIFTTFFRVAAGLSKLRLYHEVSVFDAADQLYEYINCHPGTGMLRDAVTIAEH 353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Chain B from PDB  Type:PROTEIN  Length:362
 aligned with Q76K71_RHOER | Q76K71 from UniProtKB/TrEMBL  Length:353

    Alignment length:362
                                      1                                                                                                                                                                                                                                                                                                                                                               
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  
         Q76K71_RHOER     - ----------MESAIGEHLQCPRTLTRRVPDTYTPPFPMWVGRADDALQQVVMGYLGVQFRDEDQRPAALQAMRDIVAGFDLPDGPAHHDLTHHIDNQGYENLIVVGYWKDVSSQHRWSTSTPIASWWESEDRLSDGLGFFREIVAPRAEQFETLYAFQEDLPGVGAVMDGISGEINEHGYWGSMRERFPISQTDWMQASGELRVIAGDPAVGGRVVVRGHDNIALIRSGQDWADAEADERSLYLDEILPTLQSGMDFLRDNGPAVGCYSNRFVRNIDIDGNFLDLSYNIGHWASLDQLERWSESHPTHLRIFTTFFRVAAGLSKLRLYHEVSVFDAADQLYEYINCHPGTGMLRDAVTIAE 352
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh....hhhhh.....................ee........eeeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhh.eeeee......hhhhhhh.ee..........hhhhhhhhhhhh.........eeee.hhhhh.eeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee.....eeeeeeeeeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhh...eeeeeeeeehhh.eeeeee.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a15 B  -9 SSGLVPRGSHMESAIGEHLQCPRTLTRRVPDTYTPPFPMWVGRADDALQQVVMGYLGVQFRDEDQRPAALQAMRDIVAGFDLPDGPAHHDLTHHIDNQGYENLIVVGYWKDVSSQHRWSTSTPIASWWESEDRLSDGLGFFREIVAPRAEQFETLYAFQEDLPGVGAVMDGISGEINEHGYWGSMRERFPISQTDWMQASGELRVIAGDPAVGGRVVVRGHDNIALIRSGQDWADAEADERSLYLDEILPTLQSGMDFLRDNGPAVGCYSNRFVRNIDIDGNFLDLSYNIGHWASLDQLERWSESHPTHLRIFTTFFRVAAGLSKLRLYHEVSVFDAADQLYEYINCHPGTGMLRDAVTIAE 352
                                     0        10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Chain C from PDB  Type:PROTEIN  Length:353
 aligned with Q76K71_RHOER | Q76K71 from UniProtKB/TrEMBL  Length:353

    Alignment length:353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   
         Q76K71_RHOER     1 MESAIGEHLQCPRTLTRRVPDTYTPPFPMWVGRADDALQQVVMGYLGVQFRDEDQRPAALQAMRDIVAGFDLPDGPAHHDLTHHIDNQGYENLIVVGYWKDVSSQHRWSTSTPIASWWESEDRLSDGLGFFREIVAPRAEQFETLYAFQEDLPGVGAVMDGISGEINEHGYWGSMRERFPISQTDWMQASGELRVIAGDPAVGGRVVVRGHDNIALIRSGQDWADAEADERSLYLDEILPTLQSGMDFLRDNGPAVGCYSNRFVRNIDIDGNFLDLSYNIGHWASLDQLERWSESHPTHLRIFTTFFRVAAGLSKLRLYHEVSVFDAADQLYEYINCHPGTGMLRDAVTIAEH 353
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhh.....................ee........eeeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeee.....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..hhh.eeeee......hhhhhhh.ee..........hhhhhhhhhhhh.........eeeeee...eeeeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeehhh.eeeeee.....hhhhh...hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a15 C   1 MESAIGEHLQCPRTLTRRVPDTYTPPFPMWVGRADDALQQVVMGYLGVQFRDEDQRPAALQAMRDIVAGFDLPDGPAHHDLTHHIDNQGYENLIVVGYWKDVSSQHRWSTSTPIASWWESEDRLSDGLGFFREIVAPRAEQFETLYAFQEDLPGVGAVMDGISGEINEHGYWGSMRERFPISQTDWMQASGELRVIAGDPAVGGRVVVRGHDNIALIRSGQDWADAEADERSLYLDEILPTLQSGMDFLRDNGPAVGCYSNRFVRNIDIDGNFLDLSYNIGHWASLDQLERWSESHPTHLRIFTTFFRVAAGLSKLRLYHEVSVFDAADQLYEYINCHPGTGMLRDAVTIAEH 353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

Chain D from PDB  Type:PROTEIN  Length:362
 aligned with Q76K71_RHOER | Q76K71 from UniProtKB/TrEMBL  Length:353

    Alignment length:362
                                      1                                                                                                                                                                                                                                                                                                                                                               
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350  
         Q76K71_RHOER     - ----------MESAIGEHLQCPRTLTRRVPDTYTPPFPMWVGRADDALQQVVMGYLGVQFRDEDQRPAALQAMRDIVAGFDLPDGPAHHDLTHHIDNQGYENLIVVGYWKDVSSQHRWSTSTPIASWWESEDRLSDGLGFFREIVAPRAEQFETLYAFQEDLPGVGAVMDGISGEINEHGYWGSMRERFPISQTDWMQASGELRVIAGDPAVGGRVVVRGHDNIALIRSGQDWADAEADERSLYLDEILPTLQSGMDFLRDNGPAVGCYSNRFVRNIDIDGNFLDLSYNIGHWASLDQLERWSESHPTHLRIFTTFFRVAAGLSKLRLYHEVSVFDAADQLYEYINCHPGTGMLRDAVTIAE 352
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh....hhhhh.....................ee........eeeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeeee.....eeeeeeeee.hhhhhhhhhh...hhhhhh.hhhhhh..eeeeeee..hhh.eeeee......hhhhhhh.ee..........hhhhhhhhhhhh.........eeee.hhhhh.eeeee....eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeeeeeeeee.....eeeeeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeehhh.eeeeee.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a15 D  -9 SSGLVPRGSHMESAIGEHLQCPRTLTRRVPDTYTPPFPMWVGRADDALQQVVMGYLGVQFRDEDQRPAALQAMRDIVAGFDLPDGPAHHDLTHHIDNQGYENLIVVGYWKDVSSQHRWSTSTPIASWWESEDRLSDGLGFFREIVAPRAEQFETLYAFQEDLPGVGAVMDGISGEINEHGYWGSMRERFPISQTDWMQASGELRVIAGDPAVGGRVVVRGHDNIALIRSGQDWADAEADERSLYLDEILPTLQSGMDFLRDNGPAVGCYSNRFVRNIDIDGNFLDLSYNIGHWASLDQLERWSESHPTHLRIFTTFFRVAAGLSKLRLYHEVSVFDAADQLYEYINCHPGTGMLRDAVTIAE 352
                                     0        10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

3a16	ALDOXIME DEHYDRATASE (OXDRE) IN COMPLEX WITH PROPIONALDOXIME (SOAKED CRYSTAL)
3a17	ALDOXIME DEHYDRATASE (OXDRE) IN COMPLEX WITH BUTYRALDOXIME (CO-CRYSTAL)
3a18	ALDOXIME DEHYDRATASE (OXDRE) IN COMPLEX WITH BUTYRALDOXIME (SOAKED CRYSTAL)

Description