2PZK - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE BORDETELLA BRONCHISEPTICA ENZYME WBMG IN COMPLEX WITH NAD

Authors :   J. D. King, N. J. Harmer, D. J. Maskell, T. L. Blundell

Date :   18 May 07 (Deposition) - 02 Oct 07 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Rossmann Fold, Protein-Nad Complex, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. King, N. J. Harmer, A. Preston, C. M. Palmer, M. Rejzek, R. A. Field T. L. Blundell, D. J. Maskell
Predicting Protein Function From Structure--The Roles Of Short-Chain Dehydrogenase/Reductase Enzymes In Bordetella O-Antigen Biosynthesis.
J. Mol. Biol. V. 374 749 2007
PubMed-ID: 17950751 | Reference-DOI: 10.1016/J.JMB.2007.09.055
(for further references see the PDB file header)

Molecule 1 - PUTATIVE NUCLEOTIDE SUGAR EPIMERASE/ DEHYDRATASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	BBLPS1.15, WBMG
	Organism Scientific	:	BORDETELLA BRONCHISEPTICA
	Organism Taxid	:	518

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 3)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	NAD	2	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:140	BINDING SITE FOR RESIDUE MG A 501
2	AC2	SOFTWARE	GLY B:7 , ALA B:9 , GLY B:10 , CYS B:11 , LEU B:12 , ASP B:31 , ASN B:32 , PHE B:33 , ALA B:34 , THR B:35 , GLY B:36 , GLY B:52 , SER B:53 , VAL B:54 , SER B:75 , ALA B:76 , ALA B:77 , TYR B:79 , THR B:91 , PHE B:114 , GLN B:115 , THR B:116 , TYR B:140 , LYS B:144 , LEU B:163 , ALA B:164 , ASN B:165 , VAL B:166 , HOH B:409 , HOH B:417 , HOH B:454 , HOH B:521	BINDING SITE FOR RESIDUE NAD B 401
3	AC3	SOFTWARE	GLY A:7 , ALA A:9 , GLY A:10 , CYS A:11 , LEU A:12 , ASP A:31 , ASN A:32 , PHE A:33 , ALA A:34 , THR A:35 , GLY A:36 , GLY A:52 , SER A:53 , VAL A:54 , SER A:75 , ALA A:76 , ALA A:77 , TYR A:79 , THR A:91 , PHE A:114 , GLN A:115 , THR A:116 , TYR A:140 , LYS A:144 , LEU A:163 , ALA A:164 , VAL A:166 , HOH A:507 , HOH A:538 , HOH A:587 , HOH A:590 , HOH A:639 , HOH A:643	BINDING SITE FOR RESIDUE NAD A 401

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

Asymmetric/Biological Unit

No.	Residues
1	Val A:126	-	Pro A:127
2	Val B:-5	-	Pro B:-4
3	Val B:126	-	Pro B:127
4	Ala B:254	-	Pro B:255

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

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

(no "Exon" information available for 2PZK)

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:310
 aligned with O87988_BORBO | O87988 from UniProtKB/TrEMBL  Length:310

    Alignment length:310
                              1                                                                                                                                                                                                                                                                                                                   
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308
         O87988_BORBO     - --MRILITGGAGCLGSNLIEHWLPQGHEILVIDNFATGKREVLPPVAGLSVIEGSVTDAGLLERAFDSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGRPATVPIPIDSPTAPFTSYGISKTAGEAFLMMSDVPVVSLRLANVTGPRLAIGPIPTFYKRLKAGQKCFCSDTVRDFLDMSDFLAIADLSLQEGRPTGVFNVSTGEGHSIKEVFDVVLDYVGATLAEPVPVVAPGADDVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWYDKYGVTDIFSHLSAP 308
               SCOP domains d2pzka_ A: automated matches                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhhh.eeeeee.....hhhhh.....eeeee....hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhh................hhhhhhhhhhhhhhh.....eeeeee.eee......hhhhhhhhhhhh.....ee..ee.eeehhhhhhhhhhhh......eeeee.....eehhhhhhhhhhhhh........ee........ee...hhhhhhhhh.....hhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzk A  -1 SHMRILITGGAGCLGSNLIEHWLPQGHEILVIDNFATGKREVLPPVAGLSVIEGSVTDAGLLERAFDSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGRPATVPIPIDSPTAPFTSYGISKTAGEAFLMMSDVPVVSLRLANVTGPRLAIGPIPTFYKRLKAGQKCFCSDTVRDFLDMSDFLAIADLSLQEGRPTGVFNVSTGEGHSIKEVFDVVLDYVGATLAEPVPVVAPGADDVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWYDKYGVTDIFSHLSAP 308
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with O87988_BORBO | O87988 from UniProtKB/TrEMBL  Length:310

    Alignment length:313
                                   1                                                                                                                                                                                                                                                                                                                 
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303   
         O87988_BORBO     - -------MRILITGGAGCLGSNLIEHWLPQGHEILVIDNFATGKREVLPPVAGLSVIEGSVTDAGLLERAFDSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGRPATVPIPIDSPTAPFTSYGISKTAGEAFLMMSDVPVVSLRLANVTGPRLAIGPIPTFYKRLKAGQKCFCSDTVRDFLDMSDFLAIADLSLQEGRPTGVFNVSTGEGHSIKEVFDVVLDYVGATLAEPVPVVAPGADDVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWYDKYGVTDIFSHLS 306
               SCOP domains d2pzkb_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhhh.eeeeee.....hhhhh.....eeeee....hhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhh................hhhhhhhhhhhhhhh.....eeeeee.eee......hhhhhhhhhhhh.........ee.eeehhhhhhhhhhhh......eeeee.....eehhhhhhhhhhhhh.---...................hhhhhhhhh.....hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzk B  -6 LVPRGSHMRILITGGAGCLGSNLIEHWLPQGHEILVIDNFATGKREVLPPVAGLSVIEGSVTDAGLLERAFDSFKPTHVVHSAAAYKDPDDWAEDAATNVQGSINVAKAASKAGVKRLLNFQTALCYGRPATVPIPIDSPTAPFTSYGISKTAGEAFLMMSDVPVVSLRLANVTGPRLAIGPIPTFYKRLKAGQKCFCSDTVRDFLDMSDFLAIADLSLQEGRPTGVFNVSTGEGHSIKEVFDVVLDYVGA---EPVPVVAPGADDVPSVVLDPSKTETEFGWKAKVDFKDTITGQLAWYDKYGVTDIFSHLS 306
                                     3        13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243|   |  253       263       273       283       293       303   
                                                                                                                                                                                                                                                                                    244 248

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) (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)

Bordetella bronchiseptica [TaxId: 518] (6)

1a	d2pzka_	A:
1b	d2pzkb_	B:

(no "CATH Domain" information available for 2PZK)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (O87988_BORBO | O87988)

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:0050662	coenzyme binding	Interacting selectively and non-covalently with a coenzyme, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
	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:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006541	glutamine metabolic process	The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala B:254 - Pro B:255	[ RasMol ]
		Val A:126 - Pro A:127	[ RasMol ]
		Val B:-5 - Pro B:-4	[ RasMol ]
		Val B:126 - Pro B:127	[ RasMol ]

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	2pzk
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(no "Related Entries Specified in the PDB File" available for 2PZK)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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