3DL2 - JenaLib

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Title :   HEXAGONAL STRUCTURE OF THE LDH DOMAIN OF HUMAN UBIQUITIN-CONJUGATING ENZYME E2-LIKE ISOFORM A

Authors :   J. R. Walker, G. V. Avvakumov, S. Xue, E. M. Newman, P. J. Finerty Jr. , C. Butler-Cole, C. Bountra, M. Wolkstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)

Date :   26 Jun 08 (Deposition) - 15 Jul 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   L-Lactate Dehydrogenase, Oxidoreductase, Ubiquitin-Protein Ligase, Alternative Splicing, Nad, Ubl Conjugation Pathway, Structural Genomics, Structural Genomics Consortium, Sgc, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Walker, G. V. Avvakumov, S. Xue, E. M. Newman, P. J. Finerty Jr. , C. Butler-Cole, C. Bountra, M. Wolkstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, S. Dhe-Paganon
Structural Investigation Into The L-Lactate Dehydrogenase Domain Of Human Ubiquitin-Conjugating Enzyme E2-Like Isoform A.
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 VARIANT 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A-LIC
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Fragment	:	L-LACTATE DEHYDROGENASE DOMAIN, RESIDUES 171-471
	Gene	:	UEVLD, UEV3
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UEV-3, EV AND LACTATE/MALATE DEHYDROGENASE DOMAIN- CONTAINING PROTEIN

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	NA	2	Ligand/Ion	SODIUM ION
2	PO4	3	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:230 , LEU A:231 , VAL A:234 , HOH A:557	BINDING SITE FOR RESIDUE NA A 501
2	AC2	SOFTWARE	HIS A:245 , HIS A:286 , HOH A:532 , HOH A:567 , SER B:365 , HIS B:366 , THR B:367	BINDING SITE FOR RESIDUE PO4 A 502
3	AC3	SOFTWARE	ASN B:230 , LEU B:231 , VAL B:234	BINDING SITE FOR RESIDUE NA B 501
4	AC4	SOFTWARE	SER A:365 , HIS A:366 , THR A:367 , HIS B:245 , HIS B:286 , HOH B:530 , HOH B:550	BINDING SITE FOR RESIDUE PO4 B 502
5	AC5	SOFTWARE	HIS A:286 , HOH A:565 , HIS B:286 , HOH B:529	BINDING SITE FOR RESIDUE PO4 B 503

(no "SS Bond" information available for 3DL2)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:294	-	Pro A:295
2	Gln B:294	-	Pro B:295

(no "SAP(SNP)/Variant" information available for 3DL2)

(no "PROSITE Motif" information available for 3DL2)

Asymmetric/Biological Unit (7, 14)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000396197	1	ENSE00001343027	chr11:18610281-18610160	122	UEVLD_HUMAN	1-14	14	0	-	-
1.2	ENST00000396197	2	ENSE00001150754	chr11:18600355-18600271	85	UEVLD_HUMAN	15-43	29	0	-	-
1.3	ENST00000396197	3	ENSE00001322441	chr11:18596959-18596894	66	UEVLD_HUMAN	43-65	23	0	-	-
1.4	ENST00000396197	4	ENSE00001106792	chr11:18591924-18591761	164	UEVLD_HUMAN	65-119	55	0	-	-
1.5	ENST00000396197	5	ENSE00001106800	chr11:18588029-18587894	136	UEVLD_HUMAN	120-165	46	0	-	-
1.6	ENST00000396197	6	ENSE00000997735	chr11:18586557-18586439	119	UEVLD_HUMAN	165-204	40	2	A:169-204 (gaps) B:169-204 (gaps)	36 36
1.8	ENST00000396197	8	ENSE00000997734	chr11:18579877-18579775	103	UEVLD_HUMAN	205-239	35	2	A:205-239 B:205-239	35 35
1.9	ENST00000396197	9	ENSE00000997739	chr11:18568597-18568427	171	UEVLD_HUMAN	239-296	58	2	A:239-296 (gaps) B:239-296 (gaps)	58 58
1.10	ENST00000396197	10	ENSE00000997736	chr11:18566343-18566170	174	UEVLD_HUMAN	296-354	59	2	A:296-354 B:296-354 (gaps)	59 59
1.11	ENST00000396197	11	ENSE00001210262	chr11:18558016-18557953	64	UEVLD_HUMAN	354-375	22	2	A:354-375 (gaps) B:354-375	22 22
1.13	ENST00000396197	13	ENSE00001524205	chr11:18556000-18555877	124	UEVLD_HUMAN	375-416	42	2	A:375-416 B:375-416	42 42
1.14	ENST00000396197	14	ENSE00001790365	chr11:18554034-18553245	790	UEVLD_HUMAN	417-471	55	2	A:417-471 (gaps) B:417-471 (gaps)	55 55

Asymmetric/Biological 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:289
 aligned with UEVLD_HUMAN | Q8IX04 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:303
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468   
          UEVLD_HUMAN   169 TNSKSWANHENKTVNKITVVGGGELGIACTLAISAKGIADRLVLLDLSEGTKGATMDLEIFNLPNVEISKDLSASAHSKVVIFTVNSLGSSQSYLDVVQSNVDMFRALVPALGHYSQHSVLLVASQPVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKVLTWSGQEEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKTTLKEDTVTEKLQSSASSIHSLQQQLKL 471
               SCOP domains d3dl2       a1 A:169-318 automated matches                                                                                                            d3dl2a2 A:319-471 automated matches                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....-------...eeeee..hhhhhhhhhhhhhhh...eeeee...hhhhh.hhhhhhhh...eeee.hhhhhh...eeee....----.hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhh.........eeeee.......eeeee.-....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee.....--hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:169-204 (gaps)     Exon 1.8  PDB: A:205-239           --------------------------------------------------------Exon 1.10  PDB: A:296-354 UniProt: 296-354                 --------------------Exon 1.13  PDB: A:375-416 UniProt: 375-416Exon 1.14  PDB: A:417-471 (gaps) UniProt: 417-471       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.9  PDB: A:239-296 (gaps) UniProt: 239-296          ---------------------------------------------------------Exon 1.11             ------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3dl2 A 169 GSSKS-------TVNKITVVGGGELGIACTLAISAKGIADRLVLLDLSEGTKGATMDLEIFNLPNVEISKDLSASAHSKVVIFTVNS----QSYLDVVQSNVDMFRALVPALGHYSQHSVLLVASQPVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKVLTWSG-EEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKTTL--DTVTEKLQSSASSIHSLQQQLKL 471
                                |    -  |    188       198       208       218       228       238       248      |  - |     268       278       288       298       308       318       328       338       348       358| |    368       378       388       398       408       418       428       438       | -|      458       468   
                              173     181                                                                       255  260                                                                                                359 |                                                                                  446  |                      
                                                                                                                                                                                                                          361                                                                                     449

Chain B from PDB  Type:PROTEIN  Length:287
 aligned with UEVLD_HUMAN | Q8IX04 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:303
                                   178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468   
          UEVLD_HUMAN   169 TNSKSWANHENKTVNKITVVGGGELGIACTLAISAKGIADRLVLLDLSEGTKGATMDLEIFNLPNVEISKDLSASAHSKVVIFTVNSLGSSQSYLDVVQSNVDMFRALVPALGHYSQHSVLLVASQPVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQTSGKEVWVIGEQGEDKVLTWSGQEEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKTTLKEDTVTEKLQSSASSIHSLQQQLKL 471
               SCOP domains d3dl2        b1 B:169-318 automated matches                                                                                                           d3dl2b2 B:319-471 au  tomated matches                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....--------..eeeee..hhhhhhhhhhhhhhh...eeeee...hhhhh.hhhhhhhh...eeee.hhhhhh...eeee....----.hhhhhhhhhhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.hhh.eee..hhhhhhhhhhhhhh......--..eeee.......eeee.......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...eeeeeeee...........eeeeeeeee..eeeee...-..-hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: B:169-204 (gaps)     Exon 1.8  PDB: B:205-239           --------------------------------------------------------Exon 1.10  PDB: B:296-354 (gaps) UniProt: 296-354          --------------------Exon 1.13  PDB: B:375-416 UniProt: 375-416Exon 1.14  PDB: B:417-471 (gaps) UniProt: 417-471       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------Exon 1.9  PDB: B:239-296 (gaps) UniProt: 239-296          ---------------------------------------------------------Exon 1.11             ------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3dl2 B 169 GSSKS--------VNKITVVGGGELGIACTLAISAKGIADRLVLLDLSEGTKGATMDLEIFNLPNVEISKDLSASAHSKVVIFTVNS----QSYLDVVQSNVDMFRALVPALGHYSQHSVLLVASQPVEIMTYVTWKLSTFPANRVIGIGCNLDSQRLQYIITNVLKAQT--KEVWVIGEQGEDKVLTWSGQEEVVSHTSQVQLSNRAMELLRVKGQRSWSVGLSVADMVDSIVNNKKKVHSVSALAKGYYDINSEVFLSLPCILGTNGVSEVIKT-LK-DTVTEKLQSSASSIHSLQQQLKL 471
                                |    -   |   188       198       208       218       228       238       248      |  - |     268       278       288       298       308       318       328       338  |    348       358       368       378       388       398       408       418       428       438     | ||-|      458       468   
                              173      182                                                                      255  260                                                                           338  |                                                                                                    444 || |                      
                                                                                                                                                                                                      341                                                                                                      446| |                      
                                                                                                                                                                                                                                                                                                                447 |                      
                                                                                                                                                                                                                                                                                                                  449

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: LDH C-terminal domain-like (172)

Superfamily: LDH C-terminal domain-like (172)

Family: automated matches (38)

Protein domain: automated matches (38)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d3dl2a2	A:319-471
1b	d3dl2b2	B:319-471

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

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Human (Homo sapiens) [TaxId: 9606] (32)

2a	d3dl2a1	A:169-318
2b	d3dl2b1	B:169-318

(no "CATH Domain" information available for 3DL2)

(no "Pfam Domain" information available for 3DL2)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (UEVLD_HUMAN | Q8IX04)

molecular function
	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:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
	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:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0006464	cellular protein modification process	The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
	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:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
cellular component
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gln A:294 - Pro A:295	[ RasMol ]
		Gln B:294 - Pro B:295	[ RasMol ]

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	3dl2
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	UEVLD_HUMAN \| Q8IX04	:	2i6t

2i6t	ORTHORHOMBIC STRUCTURE OF THE LDH DOMAIN OF HUMAN UBIQUITIN -CONJUGATING ENZYME E2-LIKE ISOFORM A

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (7, 14)

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