2IY6 - JenaLib

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Title :   1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND CITRATE

Authors :   E. Inagaki, K. Sakamoto, M. Nishio, S. Yokoyama

Date :   13 Jul 06 (Deposition) - 24 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   Oxidoreductase, 1-Pyrroline-5-Carboxylate, Citrate, Dehyrogenase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Inagaki, N. Ohshima, H. Takahashi, C. Kuroishi, S. Yokoyama, T. H. Tahirov
Crystal Structure Of Thermus Thermophilus Delta(1)- Pyrroline-5-Carboxylate Dehydrogenase.
J. Mol. Biol. V. 362 490 2006
PubMed-ID: 16934832 | Reference-DOI: 10.1016/J.JMB.2006.07.048

Molecule 1 - 1-PYRROLINE-5-CARBOXYLATE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.5.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 19)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	FLC	2	Ligand/Ion	CITRATE ANION
3	MPD	8	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	5	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (3, 45)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FLC	6	Ligand/Ion	CITRATE ANION
3	MPD	24	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	15	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:137 , ASN A:184 , PHE A:185 , LYS A:321 , CYS A:322 , SER A:323 , GLY A:477 , ALA A:478 , PHE A:485 , HOH A:2240 , HOH A:2542 , HOH A:2546 , HOH A:2577 , HOH A:2578 , HOH A:2579 , HOH A:2581	BINDING SITE FOR RESIDUE FLC A1517
02	AC2	SOFTWARE	SER A:55 , LEU A:56 , GLU A:123 , ASP A:211 , HOH A:2130 , HOH A:2219	BINDING SITE FOR RESIDUE NA A1540
03	AC3	SOFTWARE	LYS A:510 , HIS B:465	BINDING SITE FOR RESIDUE CL A1541
04	AC4	SOFTWARE	GLU B:137 , ASN B:184 , PHE B:185 , LYS B:321 , CYS B:322 , SER B:323 , GLY B:477 , ALA B:478 , PHE B:485 , HOH B:2218 , HOH B:2351 , HOH B:2507 , HOH B:2518 , HOH B:2553 , HOH B:2554	BINDING SITE FOR RESIDUE FLC B1517
05	AC5	SOFTWARE	SER B:55 , LEU B:56 , GLU B:123 , ASP B:211 , HOH B:2116 , HOH B:2409	BINDING SITE FOR RESIDUE NA B1540
06	AC6	SOFTWARE	HIS A:465 , LYS B:510	BINDING SITE FOR RESIDUE CL B1541
07	AC7	SOFTWARE	LEU A:275 , GLN A:279 , HOH A:2585 , HOH A:2586 , HOH A:2587 , MPD B:1531	BINDING SITE FOR RESIDUE MRD A1532
08	AC8	SOFTWARE	GLU A:241 , GLY A:244 , ALA A:245 , HOH A:2318	BINDING SITE FOR RESIDUE MRD A1533
09	AC9	SOFTWARE	GLN B:279 , MPD B:1533 , HOH B:2563 , HOH B:2564	BINDING SITE FOR RESIDUE MRD B1534
10	BC1	SOFTWARE	ILE B:180 , GLU B:241 , GLY B:244 , ALA B:245 , HOH B:2306	BINDING SITE FOR RESIDUE MRD B1535
11	BC2	SOFTWARE	PRO B:5 , ARG B:110 , GLU B:143 , HOH B:2228 , HOH B:2566 , HOH B:2567	BINDING SITE FOR RESIDUE MRD B1537
12	BC3	SOFTWARE	GLU A:158 , HOH A:2582 , HOH A:2583 , HOH A:2584 , PHE B:6 , TYR B:144 , ARG B:147 , ALA B:148 , HOH B:2229	BINDING SITE FOR RESIDUE MPD A1530
13	BC4	SOFTWARE	VAL A:311 , VAL A:312 , ASP A:359 , HOH A:2232	BINDING SITE FOR RESIDUE MPD A1531
14	BC5	SOFTWARE	ARG A:151 , HOH A:2588 , HOH A:2589 , HOH A:2590	BINDING SITE FOR RESIDUE MPD A1534
15	BC6	SOFTWARE	PHE A:6 , TYR A:144 , ARG A:147 , ALA A:148 , HOH A:2248 , GLU B:158 , HOH B:2555 , HOH B:2556 , HOH B:2557	BINDING SITE FOR RESIDUE MPD B1530
16	BC7	SOFTWARE	MRD A:1532 , GLU B:416 , HOH B:2324 , HOH B:2558 , HOH B:2559	BINDING SITE FOR RESIDUE MPD B1531
17	BC8	SOFTWARE	LEU A:27 , TYR A:122 , GLU A:355 , PRO B:353 , GLU B:355 , GLU B:356 , HOH B:2560	BINDING SITE FOR RESIDUE MPD B1532
18	BC9	SOFTWARE	GLU A:416 , MRD B:1534 , HOH B:2561 , HOH B:2562	BINDING SITE FOR RESIDUE MPD B1533
19	CC1	SOFTWARE	HOH A:2588 , ARG B:151 , TYR B:171 , HOH B:2533 , HOH B:2565	BINDING SITE FOR RESIDUE MPD B1536

(no "SS Bond" information available for 2IY6)

Asymmetric Unit

No.	Residues
1	Tyr A:154	-	Pro A:155
2	Tyr B:154	-	Pro B:155

(no "SAP(SNP)/Variant" information available for 2IY6)

(no "PROSITE Motif" information available for 2IY6)

(no "Exon" information available for 2IY6)

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:516
 aligned with Q5SI02_THET8 | Q5SI02 from UniProtKB/TrEMBL  Length:516

    Alignment length:516
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510      
         Q5SI02_THET8     1 MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF 516
               SCOP domains d2iy6a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2iy6A01 A:1-289,A:480-516 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                                                              2iy6A02 A:290-479 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                   2iy6A01 A:1-289,A:480-516             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhh..eee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.....eee.....hhhhhhhhh.....eeeee.hhhhhhhhhhhhh..........eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhh.....hhhhh.......hhhhhhhhhhhhhhhhh..eeee..............eeee.....hhhhh......eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee................hhhh.......hhhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2iy6 A   1 MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF 516
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510

Chain B from PDB  Type:PROTEIN  Length:516
 aligned with Q5SI02_THET8 | Q5SI02 from UniProtKB/TrEMBL  Length:516

    Alignment length:516
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510      
         Q5SI02_THET8     1 MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF 516
               SCOP domains d2iy6b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2iy6B01 B:1-289,B:480-516 Aldehyde Dehydrogenase; Chain A, domain 1                                                                                                                                                                                                                              2iy6B02 B:290-479 Aldehyde Dehydrogenase; Chain A, domain 2                                                                                                                                   2iy6B01 B:1-289,B:480-516             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhhhh...ee.eee..eee....eeeeee..eeeeeeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeeeee..eeeee......hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh.....eee.....hhhhhhhhh.....eeeee.hhhhhhhhhhhhh..........eeeee....eeeee....hhhhhhhhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh....hhhhh.......hhhhhhhhhhhhhhhhh..eeee..............eeee.....hhhhh......eeeeeee.hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh...eeee................hhhh.......hhhhhhh.eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2iy6 B   1 MTVEPFRNEPIETFQTEEARRAMREALRRVREEFGRHYPLYIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIVGPVAVGNTVIAKPAEDAVVVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRIRFINFTGSLEVGLKIYEAAGRLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEGQLVLGGKRLEGEGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEMKAVAERF 516
                                    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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: ALDH-like (168)

Superfamily: ALDH-like (168)

Family: ALDH-like (76)

Protein domain: automated matches (24)

Thermus thermophilus HB8 [TaxId: 300852] (15)

1a	d2iy6a_	A:
1b	d2iy6b_	B:

(no "Pfam Domain" information available for 2IY6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q5SI02_THET8 | Q5SI02)

molecular function
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Tyr A:154 - Pro A:155	[ RasMol ]
		Tyr B:154 - Pro B:155	[ RasMol ]

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	2iy6
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	1.5.1.12
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2bhp	CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND NAD.
2bhq	CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND PRODUCT GLUTAMATE.
2bja	CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND NADH.
2bjk	CRYSTAL ANALYSIS OF 1-PYRROLINE-5- CARBOXYLATE DEHYDROGENASE FROM THERMUS WITH BOUND NAD AND CITRATE. RELATED ID: TTK003000033.2 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 19)

Sites (19, 19)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 4)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File