3ITG - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE THE PROLINE UTILIZATION A PROLINE DEHYDROGENASE DOMAIN (PUTA86-630) INACTIVATED WITH N-PROPARGYLGLYCINE

Authors :   J. J. Tanner

Date :   28 Aug 09 (Deposition) - 12 Jan 10 (Release) - 02 Feb 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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

Keywords :   Proline Utilization A, Puta, Flavoenzyme, Mechanism-Based Inactivation, Dna-Binding, Fad, Flavoprotein, Multifunctional Enzyme, Nad, Oxidoreductase, Proline Metabolism, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Srivastava, W. Zhu, W. H. Johnson, C. P. Whitman, D. F. Becker, J. J. Tanner
The Structure Of The Proline Utilization A Proline Dehydrogenase Domain Inactivated By N-Propargylglycine Provides Insight Into Conformational Changes Induced By Substrate Binding And Flavin Reduction.
Biochemistry V. 49 560 2010
PubMed-ID: 19994913 | Reference-DOI: 10.1021/BI901717S

Molecule 1 - BIFUNCTIONAL PROTEIN PUTA
	Chains	:	A, B
	EC Number	:	1.5.99.8, 1.5.1.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET23B
	Expression System Strain	:	BL21(DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	PROLINE DEHYDROGENASE DOMAIN, RESIDUES 86-630
	Gene	:	PUTA, POAA, B1014, JW0999
	Organism Scientific	:	ESCHERICHIA COLI K-12
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	PROLINE DEHYDROGENASE, PROLINE OXIDASE, DELTA-1- PYRROLINE-5-CARBOXYLATE DEHYDROGENASE, P5C DEHYDROGENASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	FDA	2	Ligand/Ion	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
2	LYX	2	Mod. Amino Acid	N''-(2-COENZYME A)-PROPANOYL-LYSINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	FDA	1	Ligand/Ion	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
2	LYX	1	Mod. Amino Acid	N''-(2-COENZYME A)-PROPANOYL-LYSINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	FDA	1	Ligand/Ion	DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
2	LYX	1	Mod. Amino Acid	N''-(2-COENZYME A)-PROPANOYL-LYSINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:8 , LYX A:329 , ASP A:370 , ALA A:371 , GLN A:404 , TYR A:406 , ARG A:431 , VAL A:433 , LYS A:434 , GLY A:435 , ALA A:436 , TYR A:437 , TRP A:438 , TYR A:456 , THR A:457 , ARG A:458 , LYS A:459 , THR A:462 , ALA A:485 , THR A:486 , HIS A:487 , ASN A:488 , GLN A:511 , CYS A:512 , LEU A:513 , TYR A:540 , ALA A:562 , ASN A:563 , SER A:565 , PHE A:566 , HOH A:717	BINDING SITE FOR RESIDUE FDA A 2001
2	AC2	SOFTWARE	HOH B:6 , LYX B:329 , ASP B:370 , ALA B:371 , GLN B:404 , TYR B:406 , ARG B:431 , VAL B:433 , LYS B:434 , GLY B:435 , ALA B:436 , TYR B:437 , TRP B:438 , TYR B:456 , THR B:457 , ARG B:458 , LYS B:459 , THR B:462 , ALA B:485 , THR B:486 , HIS B:487 , ASN B:488 , GLN B:511 , CYS B:512 , LEU B:513 , TYR B:540 , ALA B:562 , ASN B:563 , SER B:565 , PHE B:566	BINDING SITE FOR RESIDUE FDA B 2002

(no "SS Bond" information available for 3ITG)

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

(no "SAP(SNP)/Variant" information available for 3ITG)

(no "PROSITE Motif" information available for 3ITG)

(no "Exon" information available for 3ITG)

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:399
 aligned with PUTA_ECOLI | P09546 from UniProtKB/Swiss-Prot  Length:1320

    Alignment length:524
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606    
           PUTA_ECOLI    87 PQSVSRAAITAAYRRPETEAVSMLLEQARLPQPVAEQAHKLAYQLADKLRNQKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSGEPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAYMVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDLATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLIYPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRD 610
               SCOP domains d3itga1 A:87-261                                                                                                                                                               d3itga2 A:262-610 Proline dehydrohenase domain of bifunctional PutA protein                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.------------------------------------------------------------------------------------------------------------------------......hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh.........eeeee...hhhhhh....hhhhh.....eeeeeee.hhhhhhhhhhh-----hhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3itg A  87 PQSVSRAAITAAYRRPETEAVSMLLEQARLPQPVAEQAHKLAYQLADKLRN------------------------------------------------------------------------------------------------------------------------QFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAYMVSYQQAIHAIGKASNGRGIYEGPGISIkLSALHPRYSRAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDLATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLIYPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIYAPVGTHETLLAYLVR-----GANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRD 610
                                    96       106       116       126       136|        -         -         -         -         -         -         -         -         -         -         -         - |     266       276       286       296       306       316       326  |    336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546        |-    |  566       576       586       596       606    
                                                                            137                                                                                                                      258                                                                    329-LYX                                                                                                                                                                                                                           555   561

Chain B from PDB  Type:PROTEIN  Length:401
 aligned with PUTA_ECOLI | P09546 from UniProtKB/Swiss-Prot  Length:1320

    Alignment length:524
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606    
           PUTA_ECOLI    87 PQSVSRAAITAAYRRPETEAVSMLLEQARLPQPVAEQAHKLAYQLADKLRNQKNASGRAGMVQGLLQEFSLSSQEGVALMCLAEALLRIPDKATRDALIRDKISNGNWQSHIGRSPSLFVNAATWGLLFTGKLVSTHNEASLSRSLNRIIGKSGEPLIRKGVDMAMRLMGEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAYMVSYQQAIHAIGKASNGRGIYEGPGISIKLSALHPRYSRAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDLATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLIYPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRD 610
               SCOP domains d3itgb1 B:87-261                                                                                                                                                               d3itgb2 B:262-610 Proline dehydrohenase domain of bifunctional PutA protein                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.----------------------------------------------------------------------------------------------------------------------........hhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeehhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh.........eeeee...hhhhhh....hhhhh.....eeeeeee.hhhhhhhhhhh-----hhhhhhhhhh.....hhhhhh.hhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3itg B  87 PQSVSRAAITAAYRRPETEAVSMLLEQARLPQPVAEQAHKLAYQLADKLRN----------------------------------------------------------------------------------------------------------------------GEQFVTGETIAEALANARKLEEKGFRYSYDMLGEAALTAADAQAYMVSYQQAIHAIGKASNGRGIYEGPGISIkLSALHPRYSRAQYDRVMEELYPRLKSLTLLARQYDIGINIDAEESDRLEISLDLLEKLCFEPELAGWNGIGFVIQAYQKRCPLVIDYLIDLATRSRRRLMIRLVKGAYWDSEIKRAQMDGLEGYPVYTRKVYTDVSYLACAKKLLAVPNLIYPQFATHNAHTLAAIYQLAGQNYYPGQYEFQCLHGMGEPLYEQVTGKVADGKLNRPCRIYAPVGTHETLLAYLVR-----GANTSFVNRIADTSLPLDELVADPVTAVEKLAQQEGQTGLPHPKIPLPRD 610
                                    96       106       116       126       136|        -         -         -         -         -         -         -         -         -         -         -       256       266       276       286       296       306       316       326  |    336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546        |-    |  566       576       586       596       606    
                                                                            137                                                                                                                    256                                                                      329-LYX                                                                                                                                                                                                                           555   561

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 '\|'

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

(no "Pfam Domain" information available for 3ITG)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PUTA_ECOLI | P09546)

molecular function
	GO:0003842	1-pyrroline-5-carboxylate dehydrogenase activity	Catalysis of the reaction: 1-pyrroline-5-carboxylate + NAD+ + H2O = L-glutamate + NADH + H(+).
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0004029	aldehyde dehydrogenase (NAD) activity	Catalysis of the reaction: an aldehyde + NAD+ + H2O = an acid + NADH + H+.
	GO:0000986	bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase.
	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: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: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.
	GO:0004657	proline dehydrogenase activity	Catalysis of the reaction: L-proline + acceptor = (S)-1-pyrroline-5-carboxylate + reduced acceptor.
	GO:0043565	sequence-specific DNA binding	Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0001141	transcriptional repressor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding	Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for a bacterial-type RNA polymerase in order to stop, prevent, or reduce the frequency, rate or extent of transcription from a bacterial-type RNA polymerase promoter.
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:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	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:0006561	proline biosynthetic process	The chemical reactions and pathways resulting in the formation of proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
	GO:0010133	proline catabolic process to glutamate	The chemical reactions and pathways resulting in the breakdown of proline into other compounds, including glutamate.
	GO:0006560	proline metabolic process	The chemical reactions and pathways involving proline (pyrrolidine-2-carboxylic acid), a chiral, cyclic, nonessential alpha-amino acid found in peptide linkage in proteins.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0009898	cytoplasmic side of plasma membrane	The leaflet the plasma membrane that faces the cytoplasm and any proteins embedded or anchored in it or attached to its surface.

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	3itg
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1tiw	SAME ENZYME COMPLEXED WITH PROLINE ANALOG
2ekg	RELATED ENZYME INACTIVATED BY N-PROPARGYLGLYCINE

Description

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Ligands, Modified Residues, Ions (2, 4)

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